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PDBsum entry 2okk

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Lyase PDB id
2okk
Jmol
Contents
Protein chain
483 a.a.
Ligands
ABU ×2
GOL
Waters ×92
HEADER    LYASE                                   17-JAN-07   2OKK
TITLE     THE X-RAY CRYSTAL STRUCTURE OF THE 65KDA ISOFORM OF GLUTAMIC ACID
TITLE    2 DECARBOXYLASE (GAD65)
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: GLUTAMATE DECARBOXYLASE 2;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: RESIDUES 88-584;
COMPND   5 SYNONYM: GLUTAMATE DECARBOXYLASE 65 KDA ISOFORM, GAD-65, 65 KDA
COMPND   6 GLUTAMIC ACID DECARBOXYLASE;
COMPND   7 EC: 4.1.1.15;
COMPND   8 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: GAD2, GAD65;
SOURCE   6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE;
SOURCE   7 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST;
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 4932;
SOURCE   9 EXPRESSION_SYSTEM_STRAIN: YRD-15;
SOURCE  10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  11 EXPRESSION_SYSTEM_PLASMID: PRJ
KEYWDS    PLP-DEPENDENT DECARBOXYLASE, LYASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    A.M.BUCKLE,G.FENALTI,R.H.P.LAW,J.C.WHISSTOCK
REVDAT   5   13-JUL-11 2OKK    1       VERSN
REVDAT   4   22-SEP-09 2OKK    1       HETATM
REVDAT   3   24-FEB-09 2OKK    1       VERSN
REVDAT   2   24-APR-07 2OKK    1       JRNL
REVDAT   1   27-MAR-07 2OKK    0
JRNL        AUTH   G.FENALTI,R.H.LAW,A.M.BUCKLE,C.LANGENDORF,K.TUCK,C.J.ROSADO,
JRNL        AUTH 2 N.G.FAUX,K.MAHMOOD,C.S.HAMPE,J.P.BANGA,M.WILCE,
JRNL        AUTH 3 J.SCHMIDBERGER,J.ROSSJOHN,O.EL-KABBANI,R.N.PIKE,A.I.SMITH,
JRNL        AUTH 4 I.R.MACKAY,M.J.ROWLEY,J.C.WHISSTOCK
JRNL        TITL   GABA PRODUCTION BY GLUTAMIC ACID DECARBOXYLASE IS REGULATED
JRNL        TITL 2 BY A DYNAMIC CATALYTIC LOOP.
JRNL        REF    NAT.STRUCT.MOL.BIOL.          V.  14   280 2007
JRNL        REFN                   ISSN 1545-9993
JRNL        PMID   17384644
JRNL        DOI    10.1038/NSMB1228
REMARK   2
REMARK   2 RESOLUTION.    2.30 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) : 2.30
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 37.19
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.9
REMARK   3   NUMBER OF REFLECTIONS             : 20648
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) : 0.200
REMARK   3   R VALUE            (WORKING SET) : 0.196
REMARK   3   FREE R VALUE                     : 0.256
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.200
REMARK   3   FREE R VALUE TEST SET COUNT      : 1077
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) : 2.30
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.36
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1389
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 94.85
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2470
REMARK   3   BIN FREE R VALUE SET COUNT          : 66
REMARK   3   BIN FREE R VALUE                    : 0.3540
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3770
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 20
REMARK   3   SOLVENT ATOMS            : 92
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 51.40
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -1.32000
REMARK   3    B22 (A**2) : 0.94000
REMARK   3    B33 (A**2) : 0.37000
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): 0.454
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.269
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.203
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.110
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.944
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.909
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3877 ; 0.009 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5246 ; 1.352 ; 1.965
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   480 ; 5.799 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   156 ;37.868 ;24.038
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   658 ;17.640 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    16 ;17.402 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   578 ; 0.129 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2879 ; 0.004 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1811 ; 0.203 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2611 ; 0.303 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   165 ; 0.143 ; 0.200
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):   111 ; 0.174 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    11 ; 0.117 ; 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):  2463 ; 1.021 ; 2.000
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3849 ; 1.908 ; 5.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1629 ; 3.756 ; 7.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1397 ; 5.202 ;10.000
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 : BABINET MODEL WITH MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK   3  POSITIONS
REMARK   4
REMARK   4 2OKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-07.
REMARK 100 THE RCSB ID CODE IS RCSB041251.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 01-APR-06
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 6.2
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : APS
REMARK 200  BEAMLINE                       : 17-ID
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.000
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 20717
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.300
REMARK 200  RESOLUTION RANGE LOW       (A) : 37.190
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) : 2.30
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.42
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.8
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: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2OKJ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 39.91
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHANOL, 100  MM MES, 10 MM 2-
REMARK 280  MERCAPTOETHANOL, 20 MM CACL2, PH 6.2, VAPOR DIFFUSION, HANGING
REMARK 280  DROP, TEMPERATURE 293K
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       60.00450
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       60.00450
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       39.12550
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       49.52850
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       39.12550
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       49.52850
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       60.00450
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       39.12550
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       49.52850
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       60.00450
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       39.12550
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       49.52850
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 300 REMARK: THE BIOLOGICAL UNIT (DIMER) IS GENERATED BY APPLYING
REMARK 300 CRYSTALLOGRAPHIC SYMMETRY.
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,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 13330 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 31890 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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        0.00000
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000      -60.00450
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 A 596  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     ALA A   423
REMARK 465     SER A   424
REMARK 465     TYR A   425
REMARK 465     LEU A   426
REMARK 465     PHE A   427
REMARK 465     GLN A   428
REMARK 465     GLN A   429
REMARK 465     ASP A   430
REMARK 465     LYS A   431
REMARK 465     HIS A   432
REMARK 465     TYR A   433
REMARK 465     ASP A   518
REMARK 465     ASN A   519
REMARK 465     GLU A   520
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     PHE A  91    CG   CD1  CD2  CE1  CE2  CZ
REMARK 470     ASP A 102    CG   OD1  OD2
REMARK 470     ARG A 105    CG   CD   NE   CZ   NH1  NH2
REMARK 470     GLN A 120    OE1  NE2
REMARK 470     LYS A 124    CD   CE   NZ
REMARK 470     ASN A 139    CG   OD1
REMARK 470     ASP A 151    OD1  OD2
REMARK 470     GLN A 152    CG   CD   OE1  NE2
REMARK 470     LYS A 303    CD   CE   NZ
REMARK 470     ARG A 307    CZ   NH1  NH2
REMARK 470     HIS A 422    CG   ND1  CD2  CE1  NE2
REMARK 470     LEU A 435    CG   CD1  CD2
REMARK 470     SER A 436    OG
REMARK 470     TYR A 437    CG   CD1  CD2  CE1  CE2  CZ   OH
REMARK 470     ARG A 460    NE   CZ   NH1  NH2
REMARK 470     LYS A 473    CD   CE   NZ
REMARK 470     GLU A 476    CD   OE1  OE2
REMARK 470     THR A 515    OG1  CG2
REMARK 470     GLU A 517    CG   CD   OE1  OE2
REMARK 470     GLU A 521    CD   OE1  OE2
REMARK 470     ARG A 522    CG   CD   NE   CZ   NH1  NH2
REMARK 470     MET A 523    CG   SD   CE
REMARK 470     ARG A 536    CD   NE   CZ   NH1  NH2
REMARK 470     ASP A 584    CG   OD1  OD2
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    ASN A 201       66.24     38.81
REMARK 500    ALA A 336       79.64   -101.84
REMARK 500    VAL A 340      -71.00    -94.98
REMARK 500    LLP A 396      -94.81    -84.58
REMARK 500    GLN A 403       80.21     75.74
REMARK 500    THR A 439      -37.44     94.84
REMARK 500    CYS A 446      -86.28   -106.93
REMARK 500    HIS A 501      139.38    111.29
REMARK 500    SER A 512       32.31    -90.40
REMARK 500    LEU A 513      -15.01   -152.87
REMARK 500    ASN A 555      110.41    -29.57
REMARK 500    SER A 562       -4.31   -150.92
REMARK 500    GLN A 583       81.06   -153.76
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 GLN A  500     HIS A  501                  -36.58
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    PHE A 205        22.1      L          L   OUTSIDE RANGE
REMARK 500    GLN A 403        24.0      L          L   OUTSIDE RANGE
REMARK 500    THR A 439        23.7      L          L   OUTSIDE RANGE
REMARK 500    GLN A 500        19.3      L          L   OUTSIDE RANGE
REMARK 500    HIS A 501         7.0      L          L   EXPECTING SP3
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ABU A 585
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ABU A 586
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 587
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2OKJ   RELATED DB: PDB
DBREF  2OKK A   88   584  UNP    Q05329   DCE2_HUMAN      88    584
SEQRES   1 A  497  ASN TYR ALA PHE LEU HIS ALA THR ASP LEU LEU PRO ALA
SEQRES   2 A  497  CYS ASP GLY GLU ARG PRO THR LEU ALA PHE LEU GLN ASP
SEQRES   3 A  497  VAL MET ASN ILE LEU LEU GLN TYR VAL VAL LYS SER PHE
SEQRES   4 A  497  ASP ARG SER THR LYS VAL ILE ASP PHE HIS TYR PRO ASN
SEQRES   5 A  497  GLU LEU LEU GLN GLU TYR ASN TRP GLU LEU ALA ASP GLN
SEQRES   6 A  497  PRO GLN ASN LEU GLU GLU ILE LEU MET HIS CYS GLN THR
SEQRES   7 A  497  THR LEU LYS TYR ALA ILE LYS THR GLY HIS PRO ARG TYR
SEQRES   8 A  497  PHE ASN GLN LEU SER THR GLY LEU ASP MET VAL GLY LEU
SEQRES   9 A  497  ALA ALA ASP TRP LEU THR SER THR ALA ASN THR ASN MET
SEQRES  10 A  497  PHE THR TYR GLU ILE ALA PRO VAL PHE VAL LEU LEU GLU
SEQRES  11 A  497  TYR VAL THR LEU LYS LYS MET ARG GLU ILE ILE GLY TRP
SEQRES  12 A  497  PRO GLY GLY SER GLY ASP GLY ILE PHE SER PRO GLY GLY
SEQRES  13 A  497  ALA ILE SER ASN MET TYR ALA MET MET ILE ALA ARG PHE
SEQRES  14 A  497  LYS MET PHE PRO GLU VAL LYS GLU LYS GLY MET ALA ALA
SEQRES  15 A  497  LEU PRO ARG LEU ILE ALA PHE THR SER GLU HIS SER HIS
SEQRES  16 A  497  PHE SER LEU LYS LYS GLY ALA ALA ALA LEU GLY ILE GLY
SEQRES  17 A  497  THR ASP SER VAL ILE LEU ILE LYS CYS ASP GLU ARG GLY
SEQRES  18 A  497  LYS MET ILE PRO SER ASP LEU GLU ARG ARG ILE LEU GLU
SEQRES  19 A  497  ALA LYS GLN LYS GLY PHE VAL PRO PHE LEU VAL SER ALA
SEQRES  20 A  497  THR ALA GLY THR THR VAL TYR GLY ALA PHE ASP PRO LEU
SEQRES  21 A  497  LEU ALA VAL ALA ASP ILE CYS LYS LYS TYR LYS ILE TRP
SEQRES  22 A  497  MET HIS VAL ASP ALA ALA TRP GLY GLY GLY LEU LEU MET
SEQRES  23 A  497  SER ARG LYS HIS LYS TRP LYS LEU SER GLY VAL GLU ARG
SEQRES  24 A  497  ALA ASN SER VAL THR TRP ASN PRO HIS LLP MET MET GLY
SEQRES  25 A  497  VAL PRO LEU GLN CYS SER ALA LEU LEU VAL ARG GLU GLU
SEQRES  26 A  497  GLY LEU MET GLN ASN CYS ASN GLN MET HIS ALA SER TYR
SEQRES  27 A  497  LEU PHE GLN GLN ASP LYS HIS TYR ASP LEU SER TYR ASP
SEQRES  28 A  497  THR GLY ASP LYS ALA LEU GLN CYS GLY ARG HIS VAL ASP
SEQRES  29 A  497  VAL PHE LYS LEU TRP LEU MET TRP ARG ALA LYS GLY THR
SEQRES  30 A  497  THR GLY PHE GLU ALA HIS VAL ASP LYS CYS LEU GLU LEU
SEQRES  31 A  497  ALA GLU TYR LEU TYR ASN ILE ILE LYS ASN ARG GLU GLY
SEQRES  32 A  497  TYR GLU MET VAL PHE ASP GLY LYS PRO GLN HIS THR ASN
SEQRES  33 A  497  VAL CYS PHE TRP TYR ILE PRO PRO SER LEU ARG THR LEU
SEQRES  34 A  497  GLU ASP ASN GLU GLU ARG MET SER ARG LEU SER LYS VAL
SEQRES  35 A  497  ALA PRO VAL ILE LYS ALA ARG MET MET GLU TYR GLY THR
SEQRES  36 A  497  THR MET VAL SER TYR GLN PRO LEU GLY ASP LYS VAL ASN
SEQRES  37 A  497  PHE PHE ARG MET VAL ILE SER ASN PRO ALA ALA THR HIS
SEQRES  38 A  497  GLN ASP ILE ASP PHE LEU ILE GLU GLU ILE GLU ARG LEU
SEQRES  39 A  497  GLY GLN ASP
MODRES 2OKK LLP A  396  LYS
HET    LLP  A 396      24
HET    ABU  A 585       7
HET    ABU  A 586       7
HET    GOL  A 587       6
HETNAM     LLP 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-
HETNAM   2 LLP  PYRIDIN-4-YLMETHANE)
HETNAM     ABU GAMMA-AMINO-BUTANOIC ACID
HETNAM     GOL GLYCEROL
HETSYN     LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
HETSYN     ABU GAMMA(AMINO)-BUTYRIC ACID
HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL   1  LLP    C14 H24 N3 O7 P
FORMUL   2  ABU    2(C4 H9 N O2)
FORMUL   4  GOL    C3 H8 O3
FORMUL   5  HOH   *92(H2 O)
HELIX    1   1 ASN A   88  LEU A   92  5                                   5
HELIX    2   2 HIS A   93  LEU A   97  5                                   5
HELIX    3   3 GLY A  103  ASP A  127  1                                  25
HELIX    4   4 TYR A  137  TYR A  145  1                                   9
HELIX    5   5 ASN A  155  ALA A  170  1                                  16
HELIX    6   6 ASP A  187  ASN A  201  1                                  15
HELIX    7   7 ALA A  210  GLY A  229  1                                  20
HELIX    8   8 TRP A  230  SER A  234  5                                   5
HELIX    9   9 GLY A  242  PHE A  259  1                                  18
HELIX   10  10 GLU A  261  GLY A  266  1                                   6
HELIX   11  11 MET A  267  LEU A  270  5                                   4
HELIX   12  12 PHE A  283  LEU A  292  1                                  10
HELIX   13  13 GLY A  295  ASP A  297  5                                   3
HELIX   14  14 ILE A  311  LYS A  325  1                                  15
HELIX   15  15 PRO A  346  LYS A  358  1                                  13
HELIX   16  16 TRP A  367  SER A  374  5                                   8
HELIX   17  17 HIS A  377  SER A  382  5                                   6
HELIX   18  18 GLY A  383  ALA A  387  5                                   5
HELIX   19  19 GLY A  413  GLN A  420  1                                   8
HELIX   20  20 ASP A  434  ASP A  438  5                                   5
HELIX   21  21 THR A  439  ALA A  443  5                                   5
HELIX   22  22 ASP A  451  ASN A  487  1                                  37
HELIX   23  23 ARG A  522  SER A  527  1                                   6
HELIX   24  24 LYS A  528  GLY A  541  1                                  14
HELIX   25  25 THR A  567  GLY A  582  1                                  16
SHEET    1   A 5 TYR A 178  PHE A 179  0
SHEET    2   A 5 MET A 544  LEU A 550  1  O  MET A 544   N  PHE A 179
SHEET    3   A 5 LYS A 553  MET A 559 -1  O  ARG A 558   N  SER A 546
SHEET    4   A 5 VAL A 504  TYR A 508 -1  N  VAL A 504   O  MET A 559
SHEET    5   A 5 TYR A 491  MET A 493 -1  N  GLU A 492   O  TRP A 507
SHEET    1   B 7 ASP A 236  SER A 240  0
SHEET    2   B 7 SER A 405  VAL A 409 -1  O  VAL A 409   N  ASP A 236
SHEET    3   B 7 SER A 389  TRP A 392 -1  N  VAL A 390   O  LEU A 408
SHEET    4   B 7 TRP A 360  ALA A 365  1  N  VAL A 363   O  THR A 391
SHEET    5   B 7 VAL A 328  THR A 335  1  N  ALA A 334   O  ASP A 364
SHEET    6   B 7 LEU A 273  SER A 278  1  N  PHE A 276   O  SER A 333
SHEET    7   B 7 VAL A 299  ILE A 302  1  O  ILE A 302   N  THR A 277
LINK         C   HIS A 395                 N   LLP A 396     1555   1555  1.33
LINK         C   LLP A 396                 N   MET A 397     1555   1555  1.33
CISPEP   1 LEU A   98    PRO A   99          0        11.19
CISPEP   2 ASP A  438    THR A  439          0         5.41
CISPEP   3 GLN A  583    ASP A  584          0         1.45
SITE     1 AC1  6 GLN A 181  LEU A 182  SER A 183  PHE A 205
SITE     2 AC1  6 THR A 339  ARG A 558
SITE     1 AC2  8 GLN A 181  LEU A 182  SER A 183  ASN A 203
SITE     2 AC2  8 HIS A 282  LLP A 396  CYS A 446  HOH A 661
SITE     1 AC3  5 GLU A 279  SER A 281  HIS A 282  PHE A 283
SITE     2 AC3  5 LYS A 286
CRYST1   78.251   99.057  120.009  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      0.012779  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010095  0.000000        0.00000
SCALE3      0.000000  0.000000  0.008333        0.00000
      
PROCHECK
Go to PROCHECK summary
 References