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PDBsum entry 3mk0

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Hydrolase PDB id
3mk0
Jmol
Contents
Protein chain
481 a.a.
Ligands
NAG-NAG ×2
NPO ×2
PO4
ACT
Metals
_ZN ×2
_MG
_CA
Waters ×527
HEADER    HYDROLASE                               13-APR-10   3MK0
TITLE     REFINEMENT OF PLACENTAL ALKALINE PHOSPHATASE COMPLEXED WITH
TITLE    2 NITROPHENYL
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: ALKALINE PHOSPHATASE, PLACENTAL TYPE;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PLACENTAL ALKALINE PHOSPHATASE 1, PLAP-1, ALKALINE
COMPND   5 PHOSPHATASE REGAN ISOZYME;
COMPND   6 EC: 3.1.3.1
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606
KEYWDS    HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    B.STEC,A.CHELTSOV,J.L.MILLAN
REVDAT   2   05-OCT-11 3MK0    1       JRNL   REMARK VERSN
REVDAT   1   19-JAN-11 3MK0    0
JRNL        AUTH   B.STEC,A.CHELTSOV,J.L.MILLAN
JRNL        TITL   REFINED STRUCTURES OF PLACENTAL ALKALINE PHOSPHATASE SHOW A
JRNL        TITL 2 CONSISTENT PATTERN OF INTERACTIONS AT THE PERIPHERAL SITE.
JRNL        REF    ACTA CRYSTALLOGR.,SECT.F      V.  66   866 2010
JRNL        REFN                   ESSN 1744-3091
JRNL        PMID   20693656
JRNL        DOI    10.1107/S1744309110019767
REMARK   0
REMARK   0 THIS ENTRY 3MK0 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL
REMARK   0 STRUCTURAL DATA R1ZEBSF DETERMINED BY AUTHORS OF THE PDB ENTRY
REMARK   0 1ZEB: P.LLINAS,E.A.STURA,A.MENEZ,Z.KISS,T.STIGBRAND,J.L.MILLAN,
REMARK   0 M.H.LE DU
REMARK   0
REMARK   0 ORIGINAL DATA REFERENCE 1
REMARK   0  PDB ID: 1ZEB
REMARK   0  AUTH   P.LLINAS,E.A.STURA,A.MENEZ,Z.KISS,T.STIGBRAND,J.L.MILLAN,
REMARK   0  AUTH 2 M.H.LE DU
REMARK   0  TITL   STRUCTURAL STUDIES OF HUMAN PLACENTAL ALKALINE PHOSPHATASE
REMARK   0  TITL 2 IN COMPLEX WITH FUNCTIONAL LIGANDS.
REMARK   0  REF    J.MOL.BIOL.                   V. 350   441 2005
REMARK   0  REFN                   ISSN 0022-2836
REMARK   0  PMID   15946677
REMARK   0  DOI    10.1016/J.JMB.2005.04.068
REMARK   2
REMARK   2 RESOLUTION.    1.90 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0019
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 70.19
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 87.0
REMARK   3   NUMBER OF REFLECTIONS             : 35479
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.137
REMARK   3   R VALUE            (WORKING SET) : 0.135
REMARK   3   FREE R VALUE                     : 0.190
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 1902
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.90
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.95
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 2646
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 89.04
REMARK   3   BIN R VALUE           (WORKING SET) : 0.1770
REMARK   3   BIN FREE R VALUE SET COUNT          : 141
REMARK   3   BIN FREE R VALUE                    : 0.2420
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3691
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 89
REMARK   3   SOLVENT ATOMS            : 527
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 21.94
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.05000
REMARK   3    B22 (A**2) : 1.04000
REMARK   3    B33 (A**2) : -0.99000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): NULL
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.136
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.085
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.410
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.972
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.944
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  4019 ; 0.010 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5450 ; 1.247 ; 1.981
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   480 ; 5.949 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   195 ;33.446 ;23.744
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   686 ;13.663 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    35 ;15.126 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   605 ; 0.083 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  3058 ; 0.004 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  2397 ; 0.208 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2786 ; 0.305 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   527 ; 0.157 ; 0.200
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):     8 ; 0.083 ; 0.200
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):   141 ; 0.196 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    61 ; 0.162 ; 0.200
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  2479 ; 0.876 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3914 ; 1.349 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1697 ; 2.266 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1536 ; 3.449 ; 4.500
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.20
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3MK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-10.
REMARK 100 THE RCSB ID CODE IS RCSB058640.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : NULL
REMARK 200  PH                             : NULL
REMARK 200  NUMBER OF CRYSTALS USED        : NULL
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : NULL
REMARK 200  RADIATION SOURCE               : NULL
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : NULL
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : NULL
REMARK 200  DETECTOR MANUFACTURER          : NULL
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200  DATA SCALING SOFTWARE          : NULL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL
REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 1ZEB
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 52.14
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -X,Y,-Z+1/2
REMARK 290       4555   X,-Y,-Z
REMARK 290       5555   X+1/2,Y+1/2,Z
REMARK 290       6555   -X+1/2,-Y+1/2,Z+1/2
REMARK 290       7555   -X+1/2,Y+1/2,-Z+1/2
REMARK 290       8555   X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       53.29700
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       53.29700
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000       44.51100
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       56.94700
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       44.51100
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       56.94700
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       53.29700
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       44.51100
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       56.94700
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       53.29700
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       44.51100
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       56.94700
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 11920 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 33010 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -181.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000       89.02200
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       53.29700
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH A1148  LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     THR A   482
REMARK 465     THR A   483
REMARK 465     ASP A   484
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH A  1219     O    HOH A  1456              2.18
REMARK 500   OE2  GLU A    18     O    HOH A  1221              2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    PHE A 107      124.70    -27.56
REMARK 500    ASN A 119       18.93     58.28
REMARK 500    SER A 359     -163.07   -106.37
REMARK 500    VAL A 361       40.89    -80.62
REMARK 500    ALA A 473       48.22    -91.89
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A1330        DISTANCE =  7.33 ANGSTROMS
REMARK 525    HOH A1533        DISTANCE =  6.34 ANGSTROMS
REMARK 525    HOH A1556        DISTANCE =  6.16 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              ZN A 902  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A  42   OD1
REMARK 620 2 HIS A 358   NE2 117.4
REMARK 620 3 ASP A 357   OD2  96.5  95.4
REMARK 620 4 SEP A  92   OG  121.3 121.1  82.0
REMARK 620 5 SEP A  92   O3P  99.4  97.2 152.2  70.3
REMARK 620 N                    1     2     3     4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 903  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 311   OE2
REMARK 620 2 ASP A  42   OD2  98.3
REMARK 620 3 HOH A1003   O    97.2  85.0
REMARK 620 4 HOH A1005   O   162.6  97.0  92.2
REMARK 620 5 HOH A1004   O    88.3 172.2  90.1  77.1
REMARK 620 6 SER A 155   OG   86.6  91.2 174.9  84.9  93.3
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              ZN A 901  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 432   NE2
REMARK 620 2 HIS A 320   NE2  95.4
REMARK 620 3 ASP A 316   OD1 148.6  91.5
REMARK 620 4 SEP A  92   O3P  88.9 171.9  81.3
REMARK 620 5 HOH A1002   O   110.4  99.4  98.6  85.4
REMARK 620 6 ASP A 316   OD2  92.9  91.6  56.3  81.3 153.0
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 905  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 270   OE2
REMARK 620 2 PHE A 269   O    82.3
REMARK 620 3 GLU A 216   OE1 100.3  83.6
REMARK 620 4 GLU A 216   OE2 103.7 137.1  53.5
REMARK 620 5 HOH A1001   O   168.3  87.3  83.9  87.6
REMARK 620 6 ASP A 285   OD2  99.0 126.9 145.8  94.5  83.0
REMARK 620 7 ASP A 285   OD1  86.9  76.6 157.9 145.1  85.5  50.7
REMARK 620 N                    1     2     3     4     5     6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 803
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 804
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 903
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 905
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NPO A 912
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NPO A 913
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 950
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 934
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1ZEB   RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF ALKALINE PHOSPHATASE FROM HUMAN PLACENTA
REMARK 900 IN COMPLEX WITH 5'-AMP. THIS ENTRY 3MK0 REFLECTS AN
REMARK 900 ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA
REMARK 900 R1ZEBSF.
REMARK 900 RELATED ID: 3MK1   RELATED DB: PDB
REMARK 900 RELATED ID: 3MK2   RELATED DB: PDB
DBREF  3MK0 A    1   484  UNP    P05187   PPB1_HUMAN      23    506
SEQRES   1 A  484  ILE ILE PRO VAL GLU GLU GLU ASN PRO ASP PHE TRP ASN
SEQRES   2 A  484  ARG GLU ALA ALA GLU ALA LEU GLY ALA ALA LYS LYS LEU
SEQRES   3 A  484  GLN PRO ALA GLN THR ALA ALA LYS ASN LEU ILE ILE PHE
SEQRES   4 A  484  LEU GLY ASP GLY MET GLY VAL SER THR VAL THR ALA ALA
SEQRES   5 A  484  ARG ILE LEU LYS GLY GLN LYS LYS ASP LYS LEU GLY PRO
SEQRES   6 A  484  GLU ILE PRO LEU ALA MET ASP ARG PHE PRO TYR VAL ALA
SEQRES   7 A  484  LEU SER LYS THR TYR ASN VAL ASP LYS HIS VAL PRO ASP
SEQRES   8 A  484  SEP GLY ALA THR ALA THR ALA TYR LEU CYS GLY VAL LYS
SEQRES   9 A  484  GLY ASN PHE GLN THR ILE GLY LEU SER ALA ALA ALA ARG
SEQRES  10 A  484  PHE ASN GLN CYS ASN THR THR ARG GLY ASN GLU VAL ILE
SEQRES  11 A  484  SER VAL MET ASN ARG ALA LYS LYS ALA GLY LYS SER VAL
SEQRES  12 A  484  GLY VAL VAL THR THR THR ARG VAL GLN HIS ALA SER PRO
SEQRES  13 A  484  ALA GLY THR TYR ALA HIS THR VAL ASN ARG ASN TRP TYR
SEQRES  14 A  484  SER ASP ALA ASP VAL PRO ALA SER ALA ARG GLN GLU GLY
SEQRES  15 A  484  CYS GLN ASP ILE ALA THR GLN LEU ILE SER ASN MET ASP
SEQRES  16 A  484  ILE ASP VAL ILE LEU GLY GLY GLY ARG LYS TYR MET PHE
SEQRES  17 A  484  ARG MET GLY THR PRO ASP PRO GLU TYR PRO ASP ASP TYR
SEQRES  18 A  484  SER GLN GLY GLY THR ARG LEU ASP GLY LYS ASN LEU VAL
SEQRES  19 A  484  GLN GLU TRP LEU ALA LYS ARG GLN GLY ALA ARG TYR VAL
SEQRES  20 A  484  TRP ASN ARG THR GLU LEU MET GLN ALA SER LEU ASP PRO
SEQRES  21 A  484  SER VAL THR HIS LEU MET GLY LEU PHE GLU PRO GLY ASP
SEQRES  22 A  484  MET LYS TYR GLU ILE HIS ARG ASP SER THR LEU ASP PRO
SEQRES  23 A  484  SER LEU MET GLU MET THR GLU ALA ALA LEU ARG LEU LEU
SEQRES  24 A  484  SER ARG ASN PRO ARG GLY PHE PHE LEU PHE VAL GLU GLY
SEQRES  25 A  484  GLY ARG ILE ASP HIS GLY HIS HIS GLU SER ARG ALA TYR
SEQRES  26 A  484  ARG ALA LEU THR GLU THR ILE MET PHE ASP ASP ALA ILE
SEQRES  27 A  484  GLU ARG ALA GLY GLN LEU THR SER GLU GLU ASP THR LEU
SEQRES  28 A  484  SER LEU VAL THR ALA ASP HIS SER HIS VAL PHE SER PHE
SEQRES  29 A  484  GLY GLY TYR PRO LEU ARG GLY SER SER ILE PHE GLY LEU
SEQRES  30 A  484  ALA PRO GLY LYS ALA ARG ASP ARG LYS ALA TYR THR VAL
SEQRES  31 A  484  LEU LEU TYR GLY ASN GLY PRO GLY TYR VAL LEU LYS ASP
SEQRES  32 A  484  GLY ALA ARG PRO ASP VAL THR GLU SER GLU SER GLY SER
SEQRES  33 A  484  PRO GLU TYR ARG GLN GLN SER ALA VAL PRO LEU ASP GLU
SEQRES  34 A  484  GLU THR HIS ALA GLY GLU ASP VAL ALA VAL PHE ALA ARG
SEQRES  35 A  484  GLY PRO GLN ALA HIS LEU VAL HIS GLY VAL GLN GLU GLN
SEQRES  36 A  484  THR PHE ILE ALA HIS VAL MET ALA PHE ALA ALA CYS LEU
SEQRES  37 A  484  GLU PRO TYR THR ALA CYS ASP LEU ALA PRO PRO ALA GLY
SEQRES  38 A  484  THR THR ASP
MODRES 3MK0 ASN A  122  ASN  GLYCOSYLATION SITE
MODRES 3MK0 ASN A  249  ASN  GLYCOSYLATION SITE
MODRES 3MK0 SEP A   92  SER  PHOSPHOSERINE
HET    SEP  A  92      10
HET    NAG  A 801      14
HET    NAG  A 802      14
HET    NAG  A 803      14
HET    NAG  A 804      14
HET     ZN  A 901       1
HET     ZN  A 902       1
HET     MG  A 903       1
HET     CA  A 905       1
HET    NPO  A 912      10
HET    NPO  A 913      10
HET    PO4  A 950       5
HET    ACT  A 934       4
HETNAM     SEP PHOSPHOSERINE
HETNAM     NAG N-ACETYL-D-GLUCOSAMINE
HETNAM      ZN ZINC ION
HETNAM      MG MAGNESIUM ION
HETNAM      CA CALCIUM ION
HETNAM     NPO P-NITROPHENOL
HETNAM     PO4 PHOSPHATE ION
HETNAM     ACT ACETATE ION
HETSYN     SEP PHOSPHONOSERINE
FORMUL   1  SEP    C3 H8 N O6 P
FORMUL   2  NAG    4(C8 H15 N O6)
FORMUL   4   ZN    2(ZN 2+)
FORMUL   6   MG    MG 2+
FORMUL   7   CA    CA 2+
FORMUL   8  NPO    2(C6 H5 N O3)
FORMUL  10  PO4    O4 P 3-
FORMUL  11  ACT    C2 H3 O2 1-
FORMUL  12  HOH   *527(H2 O)
HELIX    1   1 PRO A    3  GLU A    7  5                                   5
HELIX    2   2 ASN A    8  LEU A   26  1                                  19
HELIX    3   3 GLY A   45  LYS A   60  1                                  16
HELIX    4   4 ALA A   70  PHE A   74  5                                   5
HELIX    5   5 ASP A   91  GLY A  102  1                                  12
HELIX    6   6 GLN A  120  THR A  124  5                                   5
HELIX    7   7 SER A  131  ALA A  139  1                                   9
HELIX    8   8 HIS A  153  GLY A  158  1                                   6
HELIX    9   9 SER A  170  VAL A  174  5                                   5
HELIX   10  10 PRO A  175  GLU A  181  1                                   7
HELIX   11  11 ASP A  185  ASN A  193  1                                   9
HELIX   12  12 GLY A  203  PHE A  208  5                                   6
HELIX   13  13 ASP A  220  GLY A  224  5                                   5
HELIX   14  14 ASN A  232  LYS A  240  1                                   9
HELIX   15  15 ASN A  249  LEU A  258  1                                  10
HELIX   16  16 TYR A  276  ARG A  280  5                                   5
HELIX   17  17 SER A  287  SER A  300  1                                  14
HELIX   18  18 ARG A  314  GLU A  321  1                                   8
HELIX   19  19 ARG A  323  THR A  345  1                                  23
HELIX   20  20 THR A  410  GLY A  415  1                                   6
HELIX   21  21 GLN A  445  VAL A  449  5                                   5
HELIX   22  22 THR A  456  ALA A  466  1                                  11
SHEET    1   A10 ALA A 244  VAL A 247  0
SHEET    2   A10 HIS A 264  LEU A 268  1  O  MET A 266   N  ARG A 245
SHEET    3   A10 VAL A 198  GLY A 202  1  N  ILE A 199   O  GLY A 267
SHEET    4   A10 SER A 142  ARG A 150  1  N  VAL A 145   O  LEU A 200
SHEET    5   A10 PHE A 306  GLY A 312  1  O  GLU A 311   N  VAL A 146
SHEET    6   A10 ASN A  35  GLY A  41  1  N  LEU A  40   O  VAL A 310
SHEET    7   A10 THR A 350  ALA A 356  1  O  LEU A 353   N  PHE A  39
SHEET    8   A10 VAL A 437  ARG A 442 -1  O  ARG A 442   N  SER A 352
SHEET    9   A10 TYR A  76  LYS A  81 -1  N  SER A  80   O  VAL A 437
SHEET   10   A10 VAL A 452  GLU A 454  1  O  GLN A 453   N  LYS A  81
SHEET    1   B 2 SER A 359  HIS A 360  0
SHEET    2   B 2 HIS A 432  ALA A 433 -1  O  ALA A 433   N  SER A 359
SHEET    1   C 3 PHE A 362  PHE A 364  0
SHEET    2   C 3 LEU A 391  ASN A 395 -1  O  LEU A 392   N  SER A 363
SHEET    3   C 3 SER A 423  VAL A 425  1  O  ALA A 424   N  GLY A 394
SSBOND   1 CYS A  121    CYS A  183                          1555   1555  2.03
SSBOND   2 CYS A  467    CYS A  474                          1555   1555  2.03
LINK         C   ASP A  91                 N   SEP A  92     1555   1555  1.33
LINK         C   SEP A  92                 N   GLY A  93     1555   1555  1.34
LINK         ND2 ASN A 122                 C1  NAG A 801     1555   1555  1.43
LINK         ND2 ASN A 249                 C1  NAG A 803     1555   1555  1.44
LINK         O4  NAG A 801                 C1  NAG A 802     1555   1555  1.44
LINK         O4  NAG A 803                 C1  NAG A 804     1555   1555  1.45
LINK         OD1 ASP A  42                ZN    ZN A 902     1555   1555  1.88
LINK         OE2 GLU A 311                MG  B MG A 903     1555   1555  1.92
LINK         OD2 ASP A  42                MG  B MG A 903     1555   1555  1.94
LINK         NE2 HIS A 432                ZN    ZN A 901     1555   1555  2.03
LINK        MG  B MG A 903                 O   HOH A1003     1555   1555  2.07
LINK         NE2 HIS A 358                ZN    ZN A 902     1555   1555  2.04
LINK         OD2 ASP A 357                ZN    ZN A 902     1555   1555  2.05
LINK        MG  B MG A 903                 O   HOH A1005     1555   1555  2.09
LINK        MG  B MG A 903                 O   HOH A1004     1555   1555  2.09
LINK         NE2 HIS A 320                ZN    ZN A 901     1555   1555  2.11
LINK         OD1 ASP A 316                ZN    ZN A 901     1555   1555  2.13
LINK         OG  SEP A  92                ZN    ZN A 902     1555   1555  2.16
LINK         O3P SEP A  92                ZN    ZN A 902     1555   1555  2.16
LINK         OG  SER A 155                MG  B MG A 903     1555   1555  2.16
LINK         O3P SEP A  92                ZN    ZN A 901     1555   1555  2.21
LINK        ZN    ZN A 901                 O   HOH A1002     1555   1555  2.18
LINK         OE2 GLU A 270                CA    CA A 905     1555   1555  2.26
LINK         O   PHE A 269                CA    CA A 905     1555   1555  2.39
LINK         OE1 GLU A 216                CA    CA A 905     1555   1555  2.40
LINK         OE2 GLU A 216                CA    CA A 905     1555   1555  2.44
LINK        CA    CA A 905                 O   HOH A1001     1555   1555  2.48
LINK         OD2 ASP A 285                CA    CA A 905     1555   1555  2.47
LINK         OD2 ASP A 316                ZN    ZN A 901     1555   1555  2.48
LINK         OD1 ASP A 285                CA    CA A 905     1555   1555  2.62
CISPEP   1 GLU A  469    PRO A  470          0         3.61
SITE     1 AC1  8 ASN A 122  LEU A 258  ARG A 297  NAG A 802
SITE     2 AC1  8 HOH A1124  HOH A1265  HOH A1296  HOH A1475
SITE     1 AC2  5 ARG A 301  NAG A 801  HOH A1296  HOH A1388
SITE     2 AC2  5 HOH A1396
SITE     1 AC3  7 TRP A 248  ASN A 249  GLU A 252  LEU A 284
SITE     2 AC3  7 NAG A 804  HOH A1127  HOH A1480
SITE     1 AC4  4 ASP A 403  NAG A 803  HOH A1356  HOH A1433
SITE     1 AC5  5 SEP A  92  ASP A 316  HIS A 320  HIS A 432
SITE     2 AC5  5 HOH A1002
SITE     1 AC6  5 ASP A  42  SEP A  92  ASP A 316  ASP A 357
SITE     2 AC6  5 HIS A 358
SITE     1 AC7  6 ASP A  42  SER A 155  GLU A 311  HOH A1003
SITE     2 AC7  6 HOH A1004  HOH A1005
SITE     1 AC8  5 GLU A 216  PHE A 269  GLU A 270  ASP A 285
SITE     2 AC8  5 HOH A1001
SITE     1 AC9  9 ARG A 125  GLY A 126  ARG A 250  LEU A 253
SITE     2 AC9  9 MET A 254  SER A 257  GLU A 290  ALA A 294
SITE     3 AC9  9 ARG A 297
SITE     1 BC1 11 GLY A 211  PRO A 213  PRO A 218  TYR A 221
SITE     2 BC1 11 ARG A 383  ASP A 384  TYR A 399  VAL A 400
SITE     3 BC1 11 LEU A 401  PRO A 426  HOH A1172
SITE     1 BC2  8 LYS A 275  TYR A 276  HIS A 279  ARG A 314
SITE     2 BC2  8 HOH A1138  HOH A1191  HOH A1463  HOH A1469
SITE     1 BC3  4 GLU A 277  ILE A 278  ARG A 280  HOH A1490
CRYST1   89.022  113.894  106.594  90.00  90.00  90.00 C 2 2 21      8
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.011233  0.000000  0.000000        0.00000
SCALE2      0.000000  0.008780  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009381        0.00000
      
PROCHECK
Go to PROCHECK summary
 References