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PDBsum entry 1vdn

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Isomerase/isomerase inhibitor PDB id
1vdn
Jmol
Contents
Protein chain
161 a.a.
Ligands
ACE-ALA-ALA-PRO-
ALA-MCM
Waters ×188
HEADER    ISOMERASE/ISOMERASE INHIBITOR           24-MAR-04   1VDN
TITLE     CRYSTAL STRUCTURE OF YEAST CYCLOPHILIN A COMPLEXED WITH ACE-ALA-ALA-
TITLE    2 PRO-ALA-7-AMINO-4-METHYLCOUMARIN
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CYCLOPHILIN A;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE;
COMPND   5 EC: 5.2.1.8;
COMPND   6 ENGINEERED: YES;
COMPND   7 MOL_ID: 2;
COMPND   8 MOLECULE: (ACE)AAPA(MCM);
COMPND   9 CHAIN: B;
COMPND  10 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE   3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE   4 ORGANISM_TAXID: 4932;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PET-3A;
SOURCE  10 MOL_ID: 2;
SOURCE  11 SYNTHETIC: YES;
SOURCE  12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS    BETA BARREL, ISOMERASE-ISOMERASE INHIBITOR COMPLEX, ROTAMASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.KONNO,T.SHIBANO,K.OKUDAIRA,N.TAKAHASHI
REVDAT   3   13-JUL-11 1VDN    1       VERSN
REVDAT   2   24-FEB-09 1VDN    1       VERSN
REVDAT   1   28-JUN-05 1VDN    0
JRNL        AUTH   M.KONNO,T.SHIBANO,K.OKUDAIRA,N.TAKAHASHI
JRNL        TITL   CRYSTAL STRUCTURE OF YEAST CYCLOPHILIN A COMPLEXED WITH
JRNL        TITL 2 ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARIN
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    1.60 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.0
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : ENGH & HUBER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 1.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 92.3
REMARK   3   NUMBER OF REFLECTIONS             : 17999
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.199
REMARK   3   FREE R VALUE                     : 0.237
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : 1768
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1256
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 188
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 13.50
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 14.30
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.19
REMARK   3   ESD FROM SIGMAA              (A) : 0.06
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 8.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.23
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.07
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.006
REMARK   3   BOND ANGLES            (DEGREES) : 1.37
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 24.89
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.90
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : ISOTROPIC
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1VDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-04.
REMARK 100 THE RCSB ID CODE IS RCSB006498.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 29-JUN-03
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 8.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SPRING-8
REMARK 200  BEAMLINE                       : BL38B1
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 : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 18099
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 91.7
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : 0.04800
REMARK 200  R SYM                      (I) : 0.04800
REMARK 200   FOR THE DATA SET  : 28.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.66
REMARK 200  COMPLETENESS FOR SHELL     (%) : 95.0
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : 0.08000
REMARK 200  R SYM FOR SHELL            (I) : 0.08000
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: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 1IST
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 38.36
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, METHANOL, TRIS-HCL,
REMARK 280  PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K
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       15.86850
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       56.36800
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       20.00450
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       56.36800
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       15.86850
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       20.00450
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 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 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 A     1
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     SER A   2    CB
REMARK 470     ACE B   1    CH3
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  58      -80.31   -147.01
REMARK 500    ASN A  69       13.11   -143.66
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 CHAIN B OF (ACE)AAPA(MCM)
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1IST   RELATED DB: PDB
REMARK 900 FREE YEAST CYCLOPHILIN A
DBREF  1VDN A    1   162  UNP    P14832   CYPH_YEAST       0    161
DBREF  1VDN B    1     6  PDB    1VDN     1VDN             1      6
SEQRES   1 A  162  MET SER GLN VAL TYR PHE ASP VAL GLU ALA ASP GLY GLN
SEQRES   2 A  162  PRO ILE GLY ARG VAL VAL PHE LYS LEU TYR ASN ASP ILE
SEQRES   3 A  162  VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU CYS THR
SEQRES   4 A  162  GLY GLU LYS GLY PHE GLY TYR ALA GLY SER PRO PHE HIS
SEQRES   5 A  162  ARG VAL ILE PRO ASP PHE MET LEU GLN GLY GLY ASP PHE
SEQRES   6 A  162  THR ALA GLY ASN GLY THR GLY GLY LYS SER ILE TYR GLY
SEQRES   7 A  162  GLY LYS PHE PRO ASP GLU ASN PHE LYS LYS HIS HIS ASP
SEQRES   8 A  162  ARG PRO GLY LEU LEU SER MET ALA ASN ALA GLY PRO ASN
SEQRES   9 A  162  THR ASN GLY SER GLN PHE PHE ILE THR THR VAL PRO CYS
SEQRES  10 A  162  PRO TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY GLU VAL
SEQRES  11 A  162  VAL ASP GLY TYR ASP ILE VAL LYS LYS VAL GLU SER LEU
SEQRES  12 A  162  GLY SER PRO SER GLY ALA THR LYS ALA ARG ILE VAL VAL
SEQRES  13 A  162  ALA LYS SER GLY GLU LEU
SEQRES   1 B    6  ACE ALA ALA PRO ALA MCM
HET    ACE  B   1       2
HET    MCM  B   6      13
HETNAM     ACE ACETYL GROUP
HETNAM     MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE
HETSYN     MCM 7-AMINO-4-METHYLCOUMARIN
FORMUL   2  ACE    C2 H4 O
FORMUL   2  MCM    C10 H9 N O2
FORMUL   3  HOH   *188(H2 O)
HELIX    1   1 VAL A   27  GLY A   40  1                                  14
HELIX    2   2 CYS A  117  ASP A  121  5                                   5
HELIX    3   3 GLY A  133  SER A  142  1                                  10
SHEET    1   A 8 ARG A  53  ILE A  55  0
SHEET    2   A 8 MET A  59  GLY A  62 -1  O  GLN A  61   N  ARG A  53
SHEET    3   A 8 PHE A 110  THR A 113 -1  O  ILE A 112   N  LEU A  60
SHEET    4   A 8 LEU A  95  MET A  98 -1  N  SER A  97   O  PHE A 111
SHEET    5   A 8 VAL A 126  ASP A 132 -1  O  PHE A 127   N  LEU A  96
SHEET    6   A 8 GLN A  13  LEU A  22 -1  N  VAL A  19   O  ASP A 132
SHEET    7   A 8 GLN A   3  ALA A  10 -1  N  VAL A   8   O  ILE A  15
SHEET    8   A 8 ILE A 154  GLU A 161 -1  O  LYS A 158   N  ASP A   7
LINK         C   ACE B   1                 N   ALA B   2     1555   1555  1.33
LINK         C   ALA B   5                 N   MCM B   6     1555   1555  1.34
CISPEP   1 ALA B    3    PRO B    4          0         0.53
SITE     1 AC1 23 GLN A   3  VAL A  19  ARG A  53  ILE A  55
SITE     2 AC1 23 ASP A  57  PHE A  58  GLN A  61  ASP A  91
SITE     3 AC1 23 ARG A  92  ALA A  99  ASN A 100  PHE A 111
SITE     4 AC1 23 PRO A 116  LEU A 120  HIS A 124  PRO A 146
SITE     5 AC1 23 HOH A 174  HOH A 175  HOH A 186  HOH A 274
SITE     6 AC1 23 HOH B  54  HOH B  70  HOH B 118
CRYST1   31.737   40.009  112.736  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      0.031509  0.000000  0.000000        0.00000
SCALE2      0.000000  0.024994  0.000000        0.00000
SCALE3      0.000000  0.000000  0.008870        0.00000
      
PROCHECK
Go to PROCHECK summary
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