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PDBsum entry 1fkg

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Cis-trans isomerase PDB id
1fkg
Jmol
Contents
Protein chain
107 a.a.
Ligands
SB3
Waters ×261
HEADER    CIS-TRANS ISOMERASE                     05-AUG-93   1FKG
TITLE     DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY
TITLE    2 FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR
TITLE    3 COMPLEXES WITH FKBP12
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FK506 BINDING PROTEIN;
COMPND   3 CHAIN: A;
COMPND   4 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606
KEYWDS    CIS-TRANS ISOMERASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    D.A.HOLT,J.I.LUENGO,D.S.YAMASHITA,H.-J.OH,A.L.KONIALIAN,H.-
AUTHOR   2 K.YEN,L.W.ROZAMUS,M.BRANDT,M.J.BOSSARD,M.A.LEVY,
AUTHOR   3 D.S.EGGLESTON,T.J.STOUT,J.LIANG,L.W.SCHULTZ,J.CLARDY
REVDAT   2   24-FEB-09 1FKG    1       VERSN
REVDAT   1   31-JAN-94 1FKG    0
JRNL        AUTH   D.A.HOLT,J.I.LUENGO,D.S.YAMASHITA,H.J.OH,
JRNL        AUTH 2 A.L.KONIALIAN,H.K.YEN,L.W.ROZAMUS,M.BRANDT,
JRNL        AUTH 3 M.J.BOSSARD,M.A.LEVY,D.S.EGGLESTON,J.LIANG,
JRNL        AUTH 4 L.W.SCHULTZ,T.J.STOUT,J.CLARDY
JRNL        TITL   DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF
JRNL        TITL 2 HIGH-AFFINITY FKBP LIGANDS AND THE X-RAY
JRNL        TITL 3 CRYSTAL-STRUCTURES OF THEIR COMPLEXES WITH FKBP12.
JRNL        REF    J.AM.CHEM.SOC.                V. 115  9925 1993
JRNL        REFN                   ISSN 0002-7863
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   G.D.VAN DUYNE,R.F.STANDAERT,P.A.KARPLUS,
REMARK   1  AUTH 2 S.L.SCHREIBER,J.CLARDY
REMARK   1  TITL   ATOMIC STRUCTURES OF THE HUMAN IMMUNOPHILIN
REMARK   1  TITL 2 FKBP-12 COMPLEXES WITH FK506 AND RAPAMYCIN
REMARK   1  REF    J.MOL.BIOL.                   V. 229   105 1993
REMARK   1  REFN                   ISSN 0022-2836
REMARK   2
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : X-PLOR
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : NULL
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
REMARK   3   R VALUE            (WORKING SET) : 0.184
REMARK   3   FREE R VALUE                     : NULL
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
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            : 1022
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 33
REMARK   3   SOLVENT ATOMS            : 261
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
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) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.015
REMARK   3   BOND ANGLES            (DEGREES) : 3.00
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
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  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:  THE STRUCTURE WAS SOLVED BY THE
REMARK   3  METHOD OF MOLECULAR REPLACEMENT USING X-PLOR.
REMARK   4
REMARK   4 1FKG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : NULL
REMARK 200  PH                             : NULL
REMARK 200  NUMBER OF CRYSTALS USED        : NULL
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : NULL
REMARK 200  RADIATION SOURCE               : NULL
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : NULL
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : NULL
REMARK 200  DETECTOR MANUFACTURER          : NULL
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200  DATA SCALING SOFTWARE          : NULL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL
REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 45.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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       15.78000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       38.51500
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       21.79500
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       38.51500
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       15.78000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       21.79500
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: MONOMERIC
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 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 A  18   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES
REMARK 500    ARG A  18   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.8 DEGREES
REMARK 500    ARG A  57   NE  -  CZ  -  NH1 ANGL. DEV. =   3.5 DEGREES
REMARK 500    ARG A  57   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.5 DEGREES
REMARK 500    TRP A  59   CD1 -  CG  -  CD2 ANGL. DEV. =   5.8 DEGREES
REMARK 500    TRP A  59   CE2 -  CD2 -  CG  ANGL. DEV. =  -5.2 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    ALA A  81     -116.54   -137.79
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: BP
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: NULL
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SB3 A 108
DBREF  1FKG A    1   107  UNP    P62942   FKB1A_HUMAN      1    107
SEQRES   1 A  107  GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG
SEQRES   2 A  107  THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR
SEQRES   3 A  107  THR GLY MET LEU GLU ASP GLY LYS LYS PHE ASP SER SER
SEQRES   4 A  107  ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS
SEQRES   5 A  107  GLN GLU VAL ILE ARG GLY TRP GLU GLU GLY VAL ALA GLN
SEQRES   6 A  107  MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO
SEQRES   7 A  107  ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE
SEQRES   8 A  107  PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU
SEQRES   9 A  107  LYS LEU GLU
HET    SB3  A 108      33
HETNAM     SB3 1,3-DIPHENYL-1-PROPYL-1-(3,3-DIMETHYL-1,2-
HETNAM   2 SB3  DIOXYPENTYL)-2-PIPERIDINE CARBOXYLATE
FORMUL   2  SB3    C28 H35 N O4
FORMUL   3  HOH   *87(H2 O)
HELIX    1   A ARG A   57  VAL A   63  1                                   7
SHEET    1  A1 5 VAL A   2  SER A   8  0
SHEET    2  A1 5 ARG A  71  ILE A  76 -1  O  THR A  75   N  GLN A   3
SHEET    3  A1 5 LEU A  97  LEU A 106 -1  N  LEU A  97   O  ILE A  76
SHEET    4  A1 5 THR A  21  LEU A  30 -1  N  VAL A  23   O  LYS A 105
SHEET    5  A1 5 LYS A  35  SER A  38 -1  N  PHE A  36   O  GLY A  28
SHEET    1  A2 5 VAL A   2  SER A   8  0
SHEET    2  A2 5 ARG A  71  ILE A  76 -1  O  THR A  75   N  GLN A   3
SHEET    3  A2 5 LEU A  97  LEU A 106 -1  N  LEU A  97   O  ILE A  76
SHEET    4  A2 5 THR A  21  LEU A  30 -1  N  VAL A  23   O  LYS A 105
SHEET    5  A2 5 PHE A  46  MET A  49 -1  N  PHE A  46   O  VAL A  24
SITE     1  BP  6 TYR A  26  PHE A  46  VAL A  55  ILE A  56
SITE     2  BP  6 TRP A  59  PHE A  99
SITE     1 AC1 13 ARG A  18  GLY A  19  TYR A  26  PHE A  36
SITE     2 AC1 13 ASP A  37  PHE A  46  GLY A  51  LYS A  52
SITE     3 AC1 13 VAL A  55  ILE A  56  TRP A  59  TYR A  82
SITE     4 AC1 13 PHE A  99
CRYST1   31.560   43.590   77.030  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      0.031686  0.000000  0.000000        0.00000
SCALE2      0.000000  0.022941  0.000000        0.00000
SCALE3      0.000000  0.000000  0.012982        0.00000
      
PROCHECK
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 References