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PDBsum entry 3pgd

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Top Page protein Protein-protein interface(s) links
Immune system PDB id
3pgd
Jmol
Contents
Protein chains
178 a.a.
185 a.a.
15 a.a.
Waters ×173
HEADER    IMMUNE SYSTEM                           01-NOV-10   3PGD
TITLE     CRYSTAL STRUCTURE OF HLA-DR1 WITH CLIP106-120, CANONICAL PEPTIDE
TITLE    2 ORIENTATION
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN;
COMPND   3 CHAIN: A, D;
COMPND   4 FRAGMENT: UNP RESIDUES 26-217;
COMPND   5 SYNONYM: MHC CLASS II ANTIGEN DRA;
COMPND   6 ENGINEERED: YES;
COMPND   7 MOL_ID: 2;
COMPND   8 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN;
COMPND   9 CHAIN: B, E;
COMPND  10 FRAGMENT: UNP RESIDUES 30-227;
COMPND  11 SYNONYM: MHC CLASS II ANTIGEN DRB1*1, DR-1, DR1;
COMPND  12 ENGINEERED: YES;
COMPND  13 MOL_ID: 3;
COMPND  14 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN;
COMPND  15 CHAIN: C, F;
COMPND  16 FRAGMENT: UNP RESIDUES 106-120;
COMPND  17 SYNONYM: HLA-DR ANTIGENS-ASSOCIATED INVARIANT CHAIN, IA ANTIGEN-
COMPND  18 ASSOCIATED INVARIANT CHAIN, II, P33;
COMPND  19 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: HLA-DRA, HLA-DRA1;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET11A;
SOURCE  11 MOL_ID: 2;
SOURCE  12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE  13 ORGANISM_COMMON: HUMAN;
SOURCE  14 ORGANISM_TAXID: 9606;
SOURCE  15 GENE: HLA-DRB1;
SOURCE  16 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE  17 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE  18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE  19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  20 EXPRESSION_SYSTEM_PLASMID: PET24D;
SOURCE  21 MOL_ID: 3;
SOURCE  22 SYNTHETIC: YES;
SOURCE  23 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE  24 ORGANISM_COMMON: HUMAN;
SOURCE  25 ORGANISM_TAXID: 9606
KEYWDS    MHC CLASS II, MHC II, IMMUNE SYSTEM, SELF ANTIGEN, INVARIANT CHAIN,
KEYWDS   2 CLIP
EXPDTA    X-RAY DIFFRACTION
AUTHOR    S.GUNTHER,A.SCHLUNDT,J.STICHT,Y.ROSKE,U.HEINEMANN,K.-H.WIESMULLER,
AUTHOR   2 G.JUNG,K.FALK,O.ROTZSCHKE,C.FREUND
REVDAT   2   05-JAN-11 3PGD    1       JRNL
REVDAT   1   08-DEC-10 3PGD    0
JRNL        AUTH   S.GUNTHER,A.SCHLUNDT,J.STICHT,Y.ROSKE,U.HEINEMANN,
JRNL        AUTH 2 K.H.WIESMULLER,G.JUNG,K.FALK,O.ROTZSCHKE,C.FREUND
JRNL        TITL   BIDIRECTIONAL BINDING OF INVARIANT CHAIN PEPTIDES TO AN MHC
JRNL        TITL 2 CLASS II MOLECULE.
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 107 22219 2010
JRNL        REFN                   ISSN 0027-8424
JRNL        PMID   21115828
JRNL        DOI    10.1073/PNAS.1014708107
REMARK   2
REMARK   2 RESOLUTION.    2.72 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.6.2_432)
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK   3               : ZWART
REMARK   3
REMARK   3    REFINEMENT TARGET : ML
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.72
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 33.39
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 2.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.9
REMARK   3   NUMBER OF REFLECTIONS             : 34451
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.198
REMARK   3   R VALUE            (WORKING SET) : 0.196
REMARK   3   FREE R VALUE                     : 0.242
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.010
REMARK   3   FREE R VALUE TEST SET COUNT      : 1725
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE
REMARK   3     1 33.3930 -  5.8508    0.99     3501   186  0.2031 0.2086
REMARK   3     2  5.8508 -  4.6479    1.00     3358   177  0.1644 0.2112
REMARK   3     3  4.6479 -  4.0615    1.00     3281   173  0.1469 0.2022
REMARK   3     4  4.0615 -  3.6907    1.00     3260   172  0.1786 0.2166
REMARK   3     5  3.6907 -  3.4265    1.00     3254   171  0.1966 0.2427
REMARK   3     6  3.4265 -  3.2246    1.00     3228   170  0.2102 0.2604
REMARK   3     7  3.2246 -  3.0632    1.00     3205   169  0.2257 0.3126
REMARK   3     8  3.0632 -  2.9300    1.00     3232   170  0.2353 0.2970
REMARK   3     9  2.9300 -  2.8172    1.00     3216   169  0.2654 0.3004
REMARK   3    10  2.8172 -  2.7200    1.00     3191   168  0.2784 0.3733
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
REMARK   3   SOLVENT RADIUS     : 1.10
REMARK   3   SHRINKAGE RADIUS   : 0.83
REMARK   3   K_SOL              : 0.33
REMARK   3   B_SOL              : 29.66
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.340
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 45.62
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 44.52
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 3.42450
REMARK   3    B22 (A**2) : 3.42450
REMARK   3    B33 (A**2) : -6.84910
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  TWINNING INFORMATION.
REMARK   3   FRACTION: NULL
REMARK   3   OPERATOR: NULL
REMARK   3
REMARK   3  DEVIATIONS FROM IDEAL VALUES.
REMARK   3                 RMSD          COUNT
REMARK   3   BOND      :  0.009           6321
REMARK   3   ANGLE     :  1.132           8588
REMARK   3   CHIRALITY :  0.070            931
REMARK   3   PLANARITY :  0.005           1118
REMARK   3   DIHEDRAL  : 17.141           2304
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  NCS DETAILS
REMARK   3   NUMBER OF NCS GROUPS : 3
REMARK   3   NCS GROUP : 1
REMARK   3    NCS OPERATOR : 1
REMARK   3     REFERENCE SELECTION: chain B and (resseq 0:106 or resseq 113:
REMARK   3                          190 ) and (not element H) and (not element
REMARK   3                          D)
REMARK   3     SELECTION          : chain E and (resseq 0:106 or resseq 113:
REMARK   3                          190 ) and (not element H) and (not element
REMARK   3                          D)
REMARK   3     ATOM PAIRS NUMBER  : 1503
REMARK   3     RMSD               : 0.153
REMARK   3   NCS GROUP : 2
REMARK   3    NCS OPERATOR : 1
REMARK   3     REFERENCE SELECTION: chain A and (resseq 4:44 or resseq 52:181
REMARK   3                          ) and (not element H) and (not element D)
REMARK   3     SELECTION          : chain D and (resseq 4:44 or resseq 52:181
REMARK   3                          ) and (not element H) and (not element D)
REMARK   3     ATOM PAIRS NUMBER  : 1387
REMARK   3     RMSD               : 0.131
REMARK   3   NCS GROUP : 3
REMARK   3    NCS OPERATOR : 1
REMARK   3     REFERENCE SELECTION: chain C and (resseq 106:120 ) and (not
REMARK   3                          element H) and (not element D)
REMARK   3     SELECTION          : chain F and (resseq 106:120 ) and (not
REMARK   3                          element H) and (not element D)
REMARK   3     ATOM PAIRS NUMBER  : 116
REMARK   3     RMSD               : 0.069
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3PGD COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-10.
REMARK 100 THE RCSB ID CODE IS RCSB062343.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 09-JUN-10
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 6.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : BESSY
REMARK 200  BEAMLINE                       : 14.1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.91841
REMARK 200  MONOCHROMATOR                  : SILICON
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : RAYONIX
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MXCUBE
REMARK 200  DATA SCALING SOFTWARE          : XSCALE
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 34493
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.720
REMARK 200  RESOLUTION RANGE LOW       (A) : 35.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : 0.13100
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 12.1900
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.79
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : 0.87300
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 2.200
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 62.23
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NACITRATE, BISTRIS PROPANE,
REMARK 280  PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
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   -Y+1/2,X+1/2,Z+3/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
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      137.76750
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       47.22450
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       47.22450
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000      206.65125
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       47.22450
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       47.22450
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       68.88375
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       47.22450
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       47.22450
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000      206.65125
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       47.22450
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       47.22450
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       68.88375
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000      137.76750
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F
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 A     0
REMARK 465     ILE A     1
REMARK 465     LYS A     2
REMARK 465     GLU A     3
REMARK 465     ALA A   182
REMARK 465     PRO A   183
REMARK 465     SER A   184
REMARK 465     PRO A   185
REMARK 465     LEU A   186
REMARK 465     PRO A   187
REMARK 465     GLU A   188
REMARK 465     THR A   189
REMARK 465     THR A   190
REMARK 465     GLU A   191
REMARK 465     ASN A   192
REMARK 465     GLN B   107
REMARK 465     PRO B   108
REMARK 465     LEU B   109
REMARK 465     GLN B   110
REMARK 465     HIS B   111
REMARK 465     HIS B   112
REMARK 465     ARG B   191
REMARK 465     SER B   192
REMARK 465     GLU B   193
REMARK 465     SER B   194
REMARK 465     ALA B   195
REMARK 465     GLN B   196
REMARK 465     SER B   197
REMARK 465     LYS B   198
REMARK 465     MET D     0
REMARK 465     ILE D     1
REMARK 465     LYS D     2
REMARK 465     ALA D   182
REMARK 465     PRO D   183
REMARK 465     SER D   184
REMARK 465     PRO D   185
REMARK 465     LEU D   186
REMARK 465     PRO D   187
REMARK 465     GLU D   188
REMARK 465     THR D   189
REMARK 465     THR D   190
REMARK 465     GLU D   191
REMARK 465     ASN D   192
REMARK 465     GLN E   107
REMARK 465     PRO E   108
REMARK 465     LEU E   109
REMARK 465     GLN E   110
REMARK 465     HIS E   111
REMARK 465     HIS E   112
REMARK 465     ARG E   191
REMARK 465     SER E   192
REMARK 465     GLU E   193
REMARK 465     SER E   194
REMARK 465     ALA E   195
REMARK 465     GLN E   196
REMARK 465     SER E   197
REMARK 465     LYS E   198
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     ARG A 100    CG   CD   NE   CZ   NH1  NH2
REMARK 470     LYS A 126    CG   CD   CE   NZ
REMARK 470     GLU A 158    CG   CD   OE1  OE2
REMARK 470     GLU B  22    CG   CD   OE1  OE2
REMARK 470     LYS B 105    CG   CD   CE   NZ
REMARK 470     GLU D   3    CG   CD   OE1  OE2
REMARK 470     ARG D 100    CG   CD   NE   CZ   NH1  NH2
REMARK 470     GLU D 158    CG   CD   OE1  OE2
REMARK 470     LYS E 105    CG   CD   CE   NZ
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 D   223     O    HOH D   239              2.07
REMARK 500   O    HOH B   199     O    HOH B   225              2.14
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    ARG B  23   NE  -  CZ  -  NH2 ANGL. DEV. =   3.2 DEGREES
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    GLU A  46      -38.67    -39.83
REMARK 500    LEU A  99      138.43    -40.00
REMARK 500    HIS A 143        0.36     82.83
REMARK 500    LEU A 144     -169.85    -71.24
REMARK 500    ASP B   2       76.17     82.03
REMARK 500    GLN B  64       74.73   -100.25
REMARK 500    TYR B  78      -65.34   -129.11
REMARK 500    THR B  90      -67.06   -122.10
REMARK 500    PRO B 124     -162.91    -76.78
REMARK 500    GLU D  46      -38.56    -34.98
REMARK 500    THR D 113      148.86   -174.30
REMARK 500    HIS D 143        1.21     82.90
REMARK 500    ASP E   2       78.71     82.01
REMARK 500    TYR E  78      -67.55   -129.26
REMARK 500    THR E  90      -66.17   -126.63
REMARK 500    TRP E 153       30.60     70.72
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3PGC   RELATED DB: PDB
DBREF  3PGD A    1   192  UNP    P01903   DRA_HUMAN       26    217
DBREF  3PGD B    1   198  UNP    P04229   2B11_HUMAN      30    227
DBREF  3PGD C  106   120  UNP    P04233   HG2A_HUMAN     106    120
DBREF  3PGD D    1   192  UNP    P01903   DRA_HUMAN       26    217
DBREF  3PGD E    1   198  UNP    P04229   2B11_HUMAN      30    227
DBREF  3PGD F  106   120  UNP    P04233   HG2A_HUMAN     106    120
SEQADV 3PGD MET A    0  UNP  P01903              EXPRESSION TAG
SEQADV 3PGD MET B    0  UNP  P04229              EXPRESSION TAG
SEQADV 3PGD MET D    0  UNP  P01903              EXPRESSION TAG
SEQADV 3PGD MET E    0  UNP  P04229              EXPRESSION TAG
SEQRES   1 A  193  MET ILE LYS GLU GLU HIS VAL ILE ILE GLN ALA GLU PHE
SEQRES   2 A  193  TYR LEU ASN PRO ASP GLN SER GLY GLU PHE MET PHE ASP
SEQRES   3 A  193  PHE ASP GLY ASP GLU ILE PHE HIS VAL ASP MET ALA LYS
SEQRES   4 A  193  LYS GLU THR VAL TRP ARG LEU GLU GLU PHE GLY ARG PHE
SEQRES   5 A  193  ALA SER PHE GLU ALA GLN GLY ALA LEU ALA ASN ILE ALA
SEQRES   6 A  193  VAL ASP LYS ALA ASN LEU GLU ILE MET THR LYS ARG SER
SEQRES   7 A  193  ASN TYR THR PRO ILE THR ASN VAL PRO PRO GLU VAL THR
SEQRES   8 A  193  VAL LEU THR ASN SER PRO VAL GLU LEU ARG GLU PRO ASN
SEQRES   9 A  193  VAL LEU ILE CYS PHE ILE ASP LYS PHE THR PRO PRO VAL
SEQRES  10 A  193  VAL ASN VAL THR TRP LEU ARG ASN GLY LYS PRO VAL THR
SEQRES  11 A  193  THR GLY VAL SER GLU THR VAL PHE LEU PRO ARG GLU ASP
SEQRES  12 A  193  HIS LEU PHE ARG LYS PHE HIS TYR LEU PRO PHE LEU PRO
SEQRES  13 A  193  SER THR GLU ASP VAL TYR ASP CYS ARG VAL GLU HIS TRP
SEQRES  14 A  193  GLY LEU ASP GLU PRO LEU LEU LYS HIS TRP GLU PHE ASP
SEQRES  15 A  193  ALA PRO SER PRO LEU PRO GLU THR THR GLU ASN
SEQRES   1 B  199  MET GLY ASP THR ARG PRO ARG PHE LEU TRP GLN LEU LYS
SEQRES   2 B  199  PHE GLU CYS HIS PHE PHE ASN GLY THR GLU ARG VAL ARG
SEQRES   3 B  199  LEU LEU GLU ARG CYS ILE TYR ASN GLN GLU GLU SER VAL
SEQRES   4 B  199  ARG PHE ASP SER ASP VAL GLY GLU TYR ARG ALA VAL THR
SEQRES   5 B  199  GLU LEU GLY ARG PRO ASP ALA GLU TYR TRP ASN SER GLN
SEQRES   6 B  199  LYS ASP LEU LEU GLU GLN ARG ARG ALA ALA VAL ASP THR
SEQRES   7 B  199  TYR CYS ARG HIS ASN TYR GLY VAL GLY GLU SER PHE THR
SEQRES   8 B  199  VAL GLN ARG ARG VAL GLU PRO LYS VAL THR VAL TYR PRO
SEQRES   9 B  199  SER LYS THR GLN PRO LEU GLN HIS HIS ASN LEU LEU VAL
SEQRES  10 B  199  CYS SER VAL SER GLY PHE TYR PRO GLY SER ILE GLU VAL
SEQRES  11 B  199  ARG TRP PHE ARG ASN GLY GLN GLU GLU LYS ALA GLY VAL
SEQRES  12 B  199  VAL SER THR GLY LEU ILE GLN ASN GLY ASP TRP THR PHE
SEQRES  13 B  199  GLN THR LEU VAL MET LEU GLU THR VAL PRO ARG SER GLY
SEQRES  14 B  199  GLU VAL TYR THR CYS GLN VAL GLU HIS PRO SER VAL THR
SEQRES  15 B  199  SER PRO LEU THR VAL GLU TRP ARG ALA ARG SER GLU SER
SEQRES  16 B  199  ALA GLN SER LYS
SEQRES   1 C   15  LYS MET ARG MET ALA THR PRO LEU LEU MET GLN ALA LEU
SEQRES   2 C   15  PRO MET
SEQRES   1 D  193  MET ILE LYS GLU GLU HIS VAL ILE ILE GLN ALA GLU PHE
SEQRES   2 D  193  TYR LEU ASN PRO ASP GLN SER GLY GLU PHE MET PHE ASP
SEQRES   3 D  193  PHE ASP GLY ASP GLU ILE PHE HIS VAL ASP MET ALA LYS
SEQRES   4 D  193  LYS GLU THR VAL TRP ARG LEU GLU GLU PHE GLY ARG PHE
SEQRES   5 D  193  ALA SER PHE GLU ALA GLN GLY ALA LEU ALA ASN ILE ALA
SEQRES   6 D  193  VAL ASP LYS ALA ASN LEU GLU ILE MET THR LYS ARG SER
SEQRES   7 D  193  ASN TYR THR PRO ILE THR ASN VAL PRO PRO GLU VAL THR
SEQRES   8 D  193  VAL LEU THR ASN SER PRO VAL GLU LEU ARG GLU PRO ASN
SEQRES   9 D  193  VAL LEU ILE CYS PHE ILE ASP LYS PHE THR PRO PRO VAL
SEQRES  10 D  193  VAL ASN VAL THR TRP LEU ARG ASN GLY LYS PRO VAL THR
SEQRES  11 D  193  THR GLY VAL SER GLU THR VAL PHE LEU PRO ARG GLU ASP
SEQRES  12 D  193  HIS LEU PHE ARG LYS PHE HIS TYR LEU PRO PHE LEU PRO
SEQRES  13 D  193  SER THR GLU ASP VAL TYR ASP CYS ARG VAL GLU HIS TRP
SEQRES  14 D  193  GLY LEU ASP GLU PRO LEU LEU LYS HIS TRP GLU PHE ASP
SEQRES  15 D  193  ALA PRO SER PRO LEU PRO GLU THR THR GLU ASN
SEQRES   1 E  199  MET GLY ASP THR ARG PRO ARG PHE LEU TRP GLN LEU LYS
SEQRES   2 E  199  PHE GLU CYS HIS PHE PHE ASN GLY THR GLU ARG VAL ARG
SEQRES   3 E  199  LEU LEU GLU ARG CYS ILE TYR ASN GLN GLU GLU SER VAL
SEQRES   4 E  199  ARG PHE ASP SER ASP VAL GLY GLU TYR ARG ALA VAL THR
SEQRES   5 E  199  GLU LEU GLY ARG PRO ASP ALA GLU TYR TRP ASN SER GLN
SEQRES   6 E  199  LYS ASP LEU LEU GLU GLN ARG ARG ALA ALA VAL ASP THR
SEQRES   7 E  199  TYR CYS ARG HIS ASN TYR GLY VAL GLY GLU SER PHE THR
SEQRES   8 E  199  VAL GLN ARG ARG VAL GLU PRO LYS VAL THR VAL TYR PRO
SEQRES   9 E  199  SER LYS THR GLN PRO LEU GLN HIS HIS ASN LEU LEU VAL
SEQRES  10 E  199  CYS SER VAL SER GLY PHE TYR PRO GLY SER ILE GLU VAL
SEQRES  11 E  199  ARG TRP PHE ARG ASN GLY GLN GLU GLU LYS ALA GLY VAL
SEQRES  12 E  199  VAL SER THR GLY LEU ILE GLN ASN GLY ASP TRP THR PHE
SEQRES  13 E  199  GLN THR LEU VAL MET LEU GLU THR VAL PRO ARG SER GLY
SEQRES  14 E  199  GLU VAL TYR THR CYS GLN VAL GLU HIS PRO SER VAL THR
SEQRES  15 E  199  SER PRO LEU THR VAL GLU TRP ARG ALA ARG SER GLU SER
SEQRES  16 E  199  ALA GLN SER LYS
SEQRES   1 F   15  LYS MET ARG MET ALA THR PRO LEU LEU MET GLN ALA LEU
SEQRES   2 F   15  PRO MET
FORMUL   7  HOH   *173(H2 O)
HELIX    1   1 LEU A   45  GLY A   49  5                                   5
HELIX    2   2 GLU A   55  SER A   77  1                                  23
HELIX    3   3 THR B   51  LEU B   53  5                                   3
HELIX    4   4 GLY B   54  SER B   63  1                                  10
HELIX    5   5 GLN B   64  TYR B   78  1                                  15
HELIX    6   6 TYR B   78  SER B   88  1                                  11
HELIX    7   7 LEU D   45  PHE D   51  5                                   7
HELIX    8   8 ALA D   56  SER D   77  1                                  22
HELIX    9   9 THR E   51  LEU E   53  5                                   3
HELIX   10  10 GLY E   54  SER E   63  1                                  10
HELIX   11  11 GLN E   64  TYR E   78  1                                  15
HELIX   12  12 TYR E   78  SER E   88  1                                  11
SHEET    1   A 8 GLU A  40  TRP A  43  0
SHEET    2   A 8 ASP A  29  ASP A  35 -1  N  ASP A  35   O  GLU A  40
SHEET    3   A 8 SER A  19  PHE A  26 -1  N  PHE A  26   O  ASP A  29
SHEET    4   A 8 HIS A   5  ASN A  15 -1  N  ALA A  10   O  MET A  23
SHEET    5   A 8 PHE B   7  PHE B  18 -1  O  LEU B  11   N  GLU A  11
SHEET    6   A 8 ARG B  23  TYR B  32 -1  O  LEU B  27   N  GLU B  14
SHEET    7   A 8 GLU B  35  ASP B  41 -1  O  SER B  37   N  CYS B  30
SHEET    8   A 8 TYR B  47  ALA B  49 -1  O  ARG B  48   N  ARG B  39
SHEET    1   B 4 GLU A  88  THR A  93  0
SHEET    2   B 4 ASN A 103  PHE A 112 -1  O  ILE A 106   N  LEU A  92
SHEET    3   B 4 PHE A 145  PHE A 153 -1  O  LYS A 147   N  ILE A 109
SHEET    4   B 4 SER A 133  GLU A 134 -1  N  SER A 133   O  TYR A 150
SHEET    1   C 4 GLU A  88  THR A  93  0
SHEET    2   C 4 ASN A 103  PHE A 112 -1  O  ILE A 106   N  LEU A  92
SHEET    3   C 4 PHE A 145  PHE A 153 -1  O  LYS A 147   N  ILE A 109
SHEET    4   C 4 LEU A 138  PRO A 139 -1  N  LEU A 138   O  ARG A 146
SHEET    1   D 4 LYS A 126  VAL A 128  0
SHEET    2   D 4 ASN A 118  ARG A 123 -1  N  TRP A 121   O  VAL A 128
SHEET    3   D 4 TYR A 161  GLU A 166 -1  O  ARG A 164   N  THR A 120
SHEET    4   D 4 LEU A 174  TRP A 178 -1  O  LEU A 174   N  VAL A 165
SHEET    1   E 4 LYS B  98  SER B 104  0
SHEET    2   E 4 LEU B 114  PHE B 122 -1  O  LEU B 114   N  SER B 104
SHEET    3   E 4 PHE B 155  GLU B 162 -1  O  PHE B 155   N  PHE B 122
SHEET    4   E 4 VAL B 142  SER B 144 -1  N  VAL B 143   O  MET B 160
SHEET    1   F 4 LYS B  98  SER B 104  0
SHEET    2   F 4 LEU B 114  PHE B 122 -1  O  LEU B 114   N  SER B 104
SHEET    3   F 4 PHE B 155  GLU B 162 -1  O  PHE B 155   N  PHE B 122
SHEET    4   F 4 ILE B 148  GLN B 149 -1  N  ILE B 148   O  GLN B 156
SHEET    1   G 4 GLN B 136  GLU B 138  0
SHEET    2   G 4 GLU B 128  ARG B 133 -1  N  TRP B 131   O  GLU B 138
SHEET    3   G 4 VAL B 170  GLU B 176 -1  O  THR B 172   N  PHE B 132
SHEET    4   G 4 LEU B 184  ARG B 189 -1  O  TRP B 188   N  TYR B 171
SHEET    1   H 8 GLU D  40  TRP D  43  0
SHEET    2   H 8 ASP D  29  ASP D  35 -1  N  HIS D  33   O  VAL D  42
SHEET    3   H 8 SER D  19  PHE D  26 -1  N  PHE D  26   O  ASP D  29
SHEET    4   H 8 GLU D   4  ASN D  15 -1  N  ALA D  10   O  MET D  23
SHEET    5   H 8 PHE E   7  PHE E  18 -1  O  PHE E   7   N  ASN D  15
SHEET    6   H 8 ARG E  23  TYR E  32 -1  O  LEU E  27   N  GLU E  14
SHEET    7   H 8 GLU E  35  ASP E  41 -1  O  SER E  37   N  CYS E  30
SHEET    8   H 8 TYR E  47  ALA E  49 -1  O  ARG E  48   N  ARG E  39
SHEET    1   I 4 GLU D  88  THR D  93  0
SHEET    2   I 4 ASN D 103  PHE D 112 -1  O  ILE D 106   N  LEU D  92
SHEET    3   I 4 PHE D 145  PHE D 153 -1  O  LYS D 147   N  ILE D 109
SHEET    4   I 4 SER D 133  GLU D 134 -1  N  SER D 133   O  TYR D 150
SHEET    1   J 4 GLU D  88  THR D  93  0
SHEET    2   J 4 ASN D 103  PHE D 112 -1  O  ILE D 106   N  LEU D  92
SHEET    3   J 4 PHE D 145  PHE D 153 -1  O  LYS D 147   N  ILE D 109
SHEET    4   J 4 LEU D 138  PRO D 139 -1  N  LEU D 138   O  ARG D 146
SHEET    1   K 4 LYS D 126  VAL D 128  0
SHEET    2   K 4 ASN D 118  ARG D 123 -1  N  ARG D 123   O  LYS D 126
SHEET    3   K 4 TYR D 161  GLU D 166 -1  O  ARG D 164   N  THR D 120
SHEET    4   K 4 LEU D 174  TRP D 178 -1  O  LEU D 174   N  VAL D 165
SHEET    1   L 4 LYS E  98  SER E 104  0
SHEET    2   L 4 LEU E 114  PHE E 122 -1  O  LEU E 114   N  SER E 104
SHEET    3   L 4 PHE E 155  GLU E 162 -1  O  PHE E 155   N  PHE E 122
SHEET    4   L 4 VAL E 142  SER E 144 -1  N  VAL E 143   O  MET E 160
SHEET    1   M 4 LYS E  98  SER E 104  0
SHEET    2   M 4 LEU E 114  PHE E 122 -1  O  LEU E 114   N  SER E 104
SHEET    3   M 4 PHE E 155  GLU E 162 -1  O  PHE E 155   N  PHE E 122
SHEET    4   M 4 ILE E 148  GLN E 149 -1  N  ILE E 148   O  GLN E 156
SHEET    1   N 4 GLN E 136  GLU E 138  0
SHEET    2   N 4 GLU E 128  ARG E 133 -1  N  TRP E 131   O  GLU E 138
SHEET    3   N 4 VAL E 170  GLU E 176 -1  O  THR E 172   N  PHE E 132
SHEET    4   N 4 LEU E 184  ARG E 189 -1  O  LEU E 184   N  VAL E 175
SSBOND   1 CYS A  107    CYS A  163                          1555   1555  2.06
SSBOND   2 CYS B   15    CYS B   79                          1555   1555  2.09
SSBOND   3 CYS B  117    CYS B  173                          1555   1555  2.02
SSBOND   4 CYS D  107    CYS D  163                          1555   1555  2.07
SSBOND   5 CYS E   15    CYS E   79                          1555   1555  2.07
SSBOND   6 CYS E  117    CYS E  173                          1555   1555  2.04
CISPEP   1 ASN A   15    PRO A   16          0         4.57
CISPEP   2 THR A  113    PRO A  114          0         4.41
CISPEP   3 TYR B  123    PRO B  124          0         2.99
CISPEP   4 ASN D   15    PRO D   16          0         6.58
CISPEP   5 THR D  113    PRO D  114          0         2.74
CISPEP   6 TYR E  123    PRO E  124          0         0.59
CRYST1   94.449   94.449  275.535  90.00  90.00  90.00 P 43 21 2    16
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      0.010588  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010588  0.000000        0.00000
SCALE3      0.000000  0.000000  0.003629        0.00000
MTRIX1   1  0.999877  0.012198 -0.009866        2.27236    1
MTRIX2   1  0.011905 -0.999503 -0.029205      -93.24240    1
MTRIX3   1 -0.010217  0.029084 -0.999525       70.97610    1
MTRIX1   2  0.999856  0.009774 -0.013877        2.39060    1
MTRIX2   2  0.009425 -0.999642 -0.025046      -93.57440    1
MTRIX3   2 -0.014117  0.024911 -0.999590       70.69800    1
MTRIX1   3  0.999552  0.020355 -0.021926        3.38751    1
MTRIX2   3  0.019915 -0.999599 -0.020116      -93.80250    1
MTRIX3   3 -0.022327  0.019671 -0.999557       70.39530    1
      
PROCHECK
Go to PROCHECK summary
 References