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PDBsum entry 2cio

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Hydrolase/inhibitor PDB id
2cio
Jmol
Contents
Protein chain
212 a.a.
Ligands
GLY-GLY-THR
LEU-SER-LEU-ALA
GOL ×2
ACT ×3
Waters ×161
HEADER    HYDROLASE/INHIBITOR                     24-MAR-06   2CIO
TITLE     THE HIGH RESOLUTION X-RAY STRUCTURE OF PAPAIN COMPLEXED
TITLE    2 WITH FRAGMENTS OF THE TRYPANOSOMA BRUCEI CYSTEINE PROTEASE
TITLE    3 INHIBITOR ICP.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PAPAIN;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PAPAYA PROTEINASE I, PPI, ALLERGEN, CARP1PAPAIN;
COMPND   5 EC: 3.4.22.2;
COMPND   6 MOL_ID: 2;
COMPND   7 MOLECULE: INHIBITOR OF CYSTEINE PEPTIDASE;
COMPND   8 CHAIN: B;
COMPND   9 SYNONYM: CYSTEINE PROTEASE INHIBITOR, ICP;
COMPND  10 ENGINEERED: YES;
COMPND  11 OTHER_DETAILS: TWO PEPTIDE FRAGMENTS FROM DIGESTION OF ICP
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: CARICA PAPAYA;
SOURCE   3 ORGANISM_TAXID: 3649;
SOURCE   4 OTHER_DETAILS: PURCHASED FROM SIGMA;
SOURCE   5 MOL_ID: 2;
SOURCE   6 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI;
SOURCE   7 ORGANISM_TAXID: 5691;
SOURCE   8 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   9 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE  10 EXPRESSION_SYSTEM_STRAIN: C43;
SOURCE  11 EXPRESSION_SYSTEM_PLASMID: PBP117
KEYWDS    HYDROLASE/INHIBITOR, COMPLEX HYDROLASE/INHIBITOR, ICP,
KEYWDS   2 CYSTEINE PROTEASE, INHIBITOR, TRYPANOSOMA BRUCEI,
KEYWDS   3 ALLERGEN, PROTEASE, THIOL PROTEASE, ZYMOGEN, HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.S.ALPHEY,W.N.HUNTER
REVDAT   3   24-FEB-09 2CIO    1       VERSN
REVDAT   2   14-JUN-06 2CIO    1       JRNL
REVDAT   1   18-MAY-06 2CIO    0
JRNL        AUTH   M.S.ALPHEY,W.N.HUNTER
JRNL        TITL   HIGH-RESOLUTION COMPLEX OF PAPAIN WITH REMNANTS OF
JRNL        TITL 2 A CYSTEINE PROTEASE INHIBITOR DERIVED FROM
JRNL        TITL 3 TRYPANOSOMA BRUCEI
JRNL        REF    ACTA CRYSTALLOGR.,SECT.F      V.  62   504 2006
JRNL        REFN                   ISSN 1744-3091
JRNL        PMID   16754967
JRNL        DOI    10.1107/S1744309106014849
REMARK   2
REMARK   2 RESOLUTION.    1.5  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) : 1.50
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 95.70
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0
REMARK   3   NUMBER OF REFLECTIONS             : 30823
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) : 0.179
REMARK   3   R VALUE            (WORKING SET) : 0.177
REMARK   3   FREE R VALUE                     : 0.225
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.020
REMARK   3   FREE R VALUE TEST SET COUNT      : 1551
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) : 6.69
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 95.70
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 395
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2520
REMARK   3   BIN FREE R VALUE SET COUNT          : 23
REMARK   3   BIN FREE R VALUE                    : 0.3480
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1776
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 37
REMARK   3   SOLVENT ATOMS            : 161
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 16.24
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 19.83
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.73900
REMARK   3    B22 (A**2) : 0.76400
REMARK   3    B33 (A**2) : -0.02500
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): 0.112
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.089
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.056
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.230
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.963
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.942
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  1870 ; 0.013 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  2562 ; 1.416 ; 1.956
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   246 ; 5.617 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):    90 ;34.339 ;23.444
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   291 ;13.970 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    14 ;17.949 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   261 ; 0.098 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1496 ; 0.007 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):   940 ; 0.234 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  1270 ; 0.320 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   185 ; 0.205 ; 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):    67 ; 0.230 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    19 ; 0.221 ; 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):  1158 ; 1.366 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  1817 ; 2.065 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):   839 ; 2.911 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   729 ; 3.424 ; 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 BULK SOLVENT
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3  RIDING POSITIONS. LYS211-ASN212 IS AT THE C-TERMINUS OF THE
REMARK   3  PROTEIN CHAIN WHERE ELECTRON DENSITY WAS POORLY DEFINED
REMARK   4
REMARK   4 2CIO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-06.
REMARK 100 THE PDBE ID CODE IS EBI-28267.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 08-DEC-05
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 7.50
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID29
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9756
REMARK 200  MONOCHROMATOR                  : SI(III)
REMARK 200  OPTICS                         : TOROIDAL MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 60928
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500
REMARK 200  RESOLUTION RANGE LOW       (A) : 95.700
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0
REMARK 200  DATA REDUNDANCY                : 13.600
REMARK 200  R MERGE                    (I) : 0.10000
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 21.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.58
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 13.80
REMARK 200  R MERGE FOR SHELL          (I) : 0.63000
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 3.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 9PAP
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.2
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50% ETHANOL, 0.01M NA ACETATE
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
REMARK 290       4555   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       21.16150
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       47.84850
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       23.05900
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       47.84850
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       21.16150
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       23.05900
REMARK 290   SMTRY3   4  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 GENERATING THE BIOMOLECULE
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: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 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     MET B     1
REMARK 465     SER B     2
REMARK 465     HIS B     3
REMARK 465     ASN B     4
REMARK 465     LEU B     5
REMARK 465     PHE B     6
REMARK 465     THR B     7
REMARK 465     GLU B     8
REMARK 465     GLU B     9
REMARK 465     ASP B    10
REMARK 465     ASN B    11
REMARK 465     ASN B    12
REMARK 465     LYS B    13
REMARK 465     THR B    14
REMARK 465     ILE B    15
REMARK 465     ARG B    16
REMARK 465     MET B    17
REMARK 465     VAL B    18
REMARK 465     ILE B    19
REMARK 465     GLY B    20
REMARK 465     GLU B    21
REMARK 465     THR B    22
REMARK 465     PHE B    23
REMARK 465     THR B    24
REMARK 465     ILE B    25
REMARK 465     GLU B    26
REMARK 465     LEU B    27
REMARK 465     GLU B    28
REMARK 465     SER B    29
REMARK 465     ASN B    30
REMARK 465     PRO B    31
REMARK 465     THR B    32
REMARK 465     THR B    33
REMARK 465     GLY B    34
REMARK 465     TYR B    35
REMARK 465     THR B    36
REMARK 465     TRP B    37
REMARK 465     LEU B    38
REMARK 465     ARG B    39
REMARK 465     SER B    40
REMARK 465     GLY B    41
REMARK 465     LEU B    42
REMARK 465     ALA B    43
REMARK 465     GLY B    44
REMARK 465     THR B    45
REMARK 465     GLU B    46
REMARK 465     LEU B    47
REMARK 465     SER B    48
REMARK 465     ASP B    49
REMARK 465     CYS B    50
REMARK 465     THR B    51
REMARK 465     PHE B    52
REMARK 465     ALA B    53
REMARK 465     ILE B    54
REMARK 465     GLN B    55
REMARK 465     SER B    56
REMARK 465     LYS B    57
REMARK 465     PHE B    58
REMARK 465     ASN B    59
REMARK 465     ASN B    60
REMARK 465     ARG B    61
REMARK 465     ALA B    62
REMARK 465     PRO B    63
REMARK 465     HIS B    64
REMARK 465     ASP B    65
REMARK 465     ASN B    66
REMARK 465     HIS B    67
REMARK 465     LYS B    68
REMARK 465     ASN B    69
REMARK 465     HIS B    70
REMARK 465     ARG B    71
REMARK 465     ARG B    72
REMARK 465     LEU B    73
REMARK 465     LEU B    74
REMARK 465     VAL B    75
REMARK 465     GLY B    76
REMARK 465     ALA B    77
REMARK 465     MET B    81
REMARK 465     VAL B    82
REMARK 465     LEU B    83
REMARK 465     GLU B    84
REMARK 465     VAL B    85
REMARK 465     LYS B    86
REMARK 465     ALA B    87
REMARK 465     LEU B    88
REMARK 465     LYS B    89
REMARK 465     ALA B    90
REMARK 465     GLY B    91
REMARK 465     LYS B    92
REMARK 465     HIS B    93
REMARK 465     THR B    94
REMARK 465     TYR B    99
REMARK 465     GLY B   100
REMARK 465     ARG B   101
REMARK 465     PRO B   102
REMARK 465     TRP B   103
REMARK 465     VAL B   104
REMARK 465     GLY B   105
REMARK 465     PHE B   106
REMARK 465     ASN B   107
REMARK 465     ALA B   108
REMARK 465     ALA B   109
REMARK 465     ALA B   110
REMARK 465     LYS B   111
REMARK 465     ARG B   112
REMARK 465     TYR B   113
REMARK 465     ASN B   114
REMARK 465     ILE B   115
REMARK 465     HIS B   116
REMARK 465     VAL B   117
REMARK 465     GLU B   118
REMARK 465     ALA B   119
REMARK 465     THR B   120
REMARK 465     ALA B   121
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     THR B  80    CA   C    O    CB   OG1  CG2
REMARK 470     ALA B  98    CA   C    O    CB
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   CB   ALA A    76  -  O    HOH A  2063              2.04
REMARK 500   O    HOH A  2061  -  O    HOH A  2156              1.98
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500
REMARK 500   O    HOH A  2072     O    HOH A  2140     4455      1.92
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 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    ASP A 158       14.38   -157.15
REMARK 500    SER A 205      104.11   -160.33
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 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS ARE DEFINED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1218
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1219
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1220
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1216
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1217
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1BP4   RELATED DB: PDB
REMARK 900  USE OF PAPAIN AS A MODEL FOR THE
REMARK 900  STRUCTURE-BASED DESIGN OF CATHEPSIN K
REMARK 900  INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN
REMARK 900  INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S
REMARK 900  '-SUBSITES.
REMARK 900 RELATED ID: 1BQI   RELATED DB: PDB
REMARK 900  USE OF PAPAIN AS A MODEL FOR THE
REMARK 900  STRUCTURE-BASED DESIGN OF CATHEPSIN K
REMARK 900  INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN
REMARK 900  INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S
REMARK 900  '-SUBSITES.
REMARK 900 RELATED ID: 1CVZ   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE ANALYSIS OF PAPAIN WITH
REMARK 900  CLIK148(CATHEPSIN L SPECIFIC INHIBITOR)
REMARK 900 RELATED ID: 1EFF   RELATED DB: PDB
REMARK 900  KNOWLEDGE BASED MODEL OF AN INHIBITOR BOUND
REMARK 900   TO A THIOL(CYSTEIN) PROTEASE, PAPAIN
REMARK 900  COMPLEXED WITH NAPQI
REMARK 900 RELATED ID: 1KHP   RELATED DB: PDB
REMARK 900  MONOCLINIC FORM OF PAPAIN/ZLFG-DAM COVALENT
REMARK 900   COMPLEX
REMARK 900 RELATED ID: 1KHQ   RELATED DB: PDB
REMARK 900  ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM
REMARK 900  COVALENT COMPLEX
REMARK 900 RELATED ID: 1PAD   RELATED DB: PDB
REMARK 900  PAPAIN -ACETYL-ALANYL-ALANYL- PHENYLALANYL-
REMARK 900  METHYLENYLALANYL DERIVATIVE OF CYSTEINE 25 (/
REMARK 900  ACAAPACK)
REMARK 900 RELATED ID: 1PE6   RELATED DB: PDB
REMARK 900  PAPAIN COMPLEX WITH E-64-C
REMARK 900 RELATED ID: 1PIP   RELATED DB: PDB
REMARK 900  PAPAIN COMPLEX WITH SUCCINYL-GLN-VAL-VAL-
REMARK 900  ALA-ALA-P-NITROANILIDE
REMARK 900 RELATED ID: 1POP   RELATED DB: PDB
REMARK 900  PAPAIN COMPLEX WITH LEUPEPTIN (N-ACETYL-L-
REMARK 900  LEUCYL-L-LEUCYL-L-ARGININAL)
REMARK 900 RELATED ID: 1PPD   RELATED DB: PDB
REMARK 900  2-HYDROXYETHYLTHIOPAPAIN - CRYSTAL FORM D
REMARK 900 RELATED ID: 1PPN   RELATED DB: PDB
REMARK 900  PAPAIN CYS-25 WITH BOUND ATOM
REMARK 900 RELATED ID: 1PPP   RELATED DB: PDB
REMARK 900  PAPAIN COMPLEX WITH E64-C (FORM II)
REMARK 900 RELATED ID: 1STF   RELATED DB: PDB
REMARK 900  PAPAIN (CYS 25 CARBOXYMETHYLATED) COMPLEXED
REMARK 900  WITH THE INHIBITOR STEFIN B (CYSTATIN B)
REMARK 900  MUTANT WITH CYS I 8 REPLACED BY SER (C(
REMARK 900  I 8)S)
REMARK 900 RELATED ID: 2PAD   RELATED DB: PDB
REMARK 900  PAPAIN -CYSTEINYL DERIVATIVE OF CYSTEINE-25
REMARK 900   (/PAPSSCYS)
REMARK 900 RELATED ID: 4PAD   RELATED DB: PDB
REMARK 900  PAPAIN -TOSYL-METHYLENYLLYSYL DERIVATIVE OF
REMARK 900  CYSTEINE-25 (/TLCK)
REMARK 900 RELATED ID: 5PAD   RELATED DB: PDB
REMARK 900  PAPAIN -BENZYLOXYCARBONYL-GLYCYL- PHENYLALANYL-
REMARK 900  METHYLENYLGLYCYL DERIVATIVE (/ZGPGCK)
REMARK 900 RELATED ID: 6PAD   RELATED DB: PDB
REMARK 900  PAPAIN -BENZYLOXYCARBONYL- PHENYLALANYL-
REMARK 900  METHYLENYLALANYL DERIVATIVE (/ZPACK)
REMARK 900 RELATED ID: 9PAP   RELATED DB: PDB
REMARK 900  PAPAIN CYS-25 OXIDIZED
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 PROTEIN USED IN EXPERIMENT WAS COMMERCIALLY AVAILABLE AND
REMARK 999 ALREADY HAD REMOVED SIGNAL AND PROPEPTIDE SEQUENCE FROM N-
REMARK 999 TERMINUS.
DBREF  2CIO A    1   212  UNP    P00784   PAPA1_CARPA    134    345
DBREF  2CIO B    1   121  UNP    Q868H0   Q868H0_9TRYP     1    121
SEQADV 2CIO GLN A   47  UNP  P00784    GLU   180 CONFLICT
SEQRES   1 A  212  ILE PRO GLU TYR VAL ASP TRP ARG GLN LYS GLY ALA VAL
SEQRES   2 A  212  THR PRO VAL LYS ASN GLN GLY SER CYS GLY SER OCS TRP
SEQRES   3 A  212  ALA PHE SER ALA VAL VAL THR ILE GLU GLY ILE ILE LYS
SEQRES   4 A  212  ILE ARG THR GLY ASN LEU ASN GLN TYR SER GLU GLN GLU
SEQRES   5 A  212  LEU LEU ASP CYS ASP ARG ARG SER TYR GLY CYS ASN GLY
SEQRES   6 A  212  GLY TYR PRO TRP SER ALA LEU GLN LEU VAL ALA GLN TYR
SEQRES   7 A  212  GLY ILE HIS TYR ARG ASN THR TYR PRO TYR GLU GLY VAL
SEQRES   8 A  212  GLN ARG TYR CYS ARG SER ARG GLU LYS GLY PRO TYR ALA
SEQRES   9 A  212  ALA LYS THR ASP GLY VAL ARG GLN VAL GLN PRO TYR ASN
SEQRES  10 A  212  GLU GLY ALA LEU LEU TYR SER ILE ALA ASN GLN PRO VAL
SEQRES  11 A  212  SER VAL VAL LEU GLU ALA ALA GLY LYS ASP PHE GLN LEU
SEQRES  12 A  212  TYR ARG GLY GLY ILE PHE VAL GLY PRO CYS GLY ASN LYS
SEQRES  13 A  212  VAL ASP HIS ALA VAL ALA ALA VAL GLY TYR GLY PRO ASN
SEQRES  14 A  212  TYR ILE LEU ILE LYS ASN SER TRP GLY THR GLY TRP GLY
SEQRES  15 A  212  GLU ASN GLY TYR ILE ARG ILE LYS ARG GLY THR GLY ASN
SEQRES  16 A  212  SER TYR GLY VAL CYS GLY LEU TYR THR SER SER PHE TYR
SEQRES  17 A  212  PRO VAL LYS ASN
SEQRES   1 B  121  MET SER HIS ASN LEU PHE THR GLU GLU ASP ASN ASN LYS
SEQRES   2 B  121  THR ILE ARG MET VAL ILE GLY GLU THR PHE THR ILE GLU
SEQRES   3 B  121  LEU GLU SER ASN PRO THR THR GLY TYR THR TRP LEU ARG
SEQRES   4 B  121  SER GLY LEU ALA GLY THR GLU LEU SER ASP CYS THR PHE
SEQRES   5 B  121  ALA ILE GLN SER LYS PHE ASN ASN ARG ALA PRO HIS ASP
SEQRES   6 B  121  ASN HIS LYS ASN HIS ARG ARG LEU LEU VAL GLY ALA GLY
SEQRES   7 B  121  GLY THR MET VAL LEU GLU VAL LYS ALA LEU LYS ALA GLY
SEQRES   8 B  121  LYS HIS THR LEU SER LEU ALA TYR GLY ARG PRO TRP VAL
SEQRES   9 B  121  GLY PHE ASN ALA ALA ALA LYS ARG TYR ASN ILE HIS VAL
SEQRES  10 B  121  GLU ALA THR ALA
MODRES 2CIO OCS A   25  CYS  CYSTEINESULFONIC ACID
HET    OCS  A  25       9
HET    ACT  A1218       8
HET    ACT  A1219       4
HET    ACT  A1220       4
HET    GOL  A1216       6
HET    GOL  A1217       6
HETNAM     OCS CYSTEINESULFONIC ACID
HETNAM     ACT ACETATE ION
HETNAM     GOL GLYCEROL
FORMUL   1  OCS    C3 H7 N O5 S
FORMUL   3  ACT    3(C2 H3 O2 1-)
FORMUL   6  GOL    2(C3 H8 O3)
FORMUL   8  HOH   *161(H2 O1)
HELIX    1   1 TRP A   26  GLY A   43  1                                  18
HELIX    2   2 SER A   49  ASP A   57  1                                   9
HELIX    3   3 TYR A   67  TYR A   78  1                                  12
HELIX    4   4 ASN A  117  GLN A  128  1                                  12
HELIX    5   5 GLY A  138  LEU A  143  1                                   6
HELIX    6   6 GLY A  198  LEU A  202  5                                   5
SHEET    1  AA 3 VAL A   5  ASP A   6  0
SHEET    2  AA 3 HIS A 159  GLY A 167 -1  O  TYR A 166   N  VAL A   5
SHEET    3  AA 3 VAL A 130  LEU A 134 -1  O  VAL A 130   N  ALA A 163
SHEET    1  AB 4 VAL A   5  ASP A   6  0
SHEET    2  AB 4 HIS A 159  GLY A 167 -1  O  TYR A 166   N  VAL A   5
SHEET    3  AB 4 TYR A 170  LYS A 174 -1  O  TYR A 170   N  GLY A 167
SHEET    4  AB 4 TYR A 186  LYS A 190 -1  O  ILE A 187   N  ILE A 173
SHEET    1  AC 2 GLY A 109  GLN A 112  0
SHEET    2  AC 2 PHE A 207  VAL A 210 -1  O  TYR A 208   N  ARG A 111
SSBOND   1 CYS A   22    CYS A   63                          1555   1555  2.06
SSBOND   2 CYS A   56    CYS A   95                          1555   1555  2.04
SSBOND   3 CYS A  153    CYS A  200                          1555   1555  2.07
LINK         C   SER A  24                 N   OCS A  25     1555   1555  1.33
LINK         C   OCS A  25                 N   TRP A  26     1555   1555  1.33
CISPEP   1 GLY A  151    PRO A  152          0        -1.49
CISPEP   2 LYS A  211    ASN A  212          0       -12.15
SITE     1 AC1  6 LYS A  17  ASN A  18  ARG A  83  ARG A  93
SITE     2 AC1  6 TYR A  94  HOH A2014
SITE     1 AC2  6 GLU A   3  ARG A  59  GLY A 138  LYS A 139
SITE     2 AC2  6 ASP A 140  HOH A2121
SITE     1 AC3  6 CYS A  56  TYR A  78  CYS A  95  ARG A  98
SITE     2 AC3  6 GOL A1217  HOH A2158
SITE     1 AC4  5 VAL A  13  THR A  14  PRO A  15  VAL A  16
SITE     2 AC4  5 TYR A 186
SITE     1 AC5 12 GLU A   3  TYR A   4  ARG A  59  GLN A  73
SITE     2 AC5 12 LEU A  74  GLN A  77  TYR A  78  ACT A1220
SITE     3 AC5 12 HOH A2004  HOH A2047  HOH A2050  HOH A2064
CRYST1   42.323   46.118   95.697  90.00  90.00  90.00 P 21 21 21    4
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      0.023628  0.000000  0.000000        0.00000
SCALE2      0.000000  0.021684  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010450        0.00000
      
PROCHECK
Go to PROCHECK summary
 References

 

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