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PDBsum entry 3kz7

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Isomerase/inhibitor PDB id
3kz7
Jmol
Contents
Protein chain
119 a.a.
Ligands
RAP
Waters ×171
HEADER    ISOMERASE/INHIBITOR                     08-DEC-09   3KZ7
TITLE     C-TERMINAL DOMAIN OF MURINE FKBP25 RAPAMYCIN COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FK506-BINDING PROTEIN 3;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: FK506-LIKE BINDING DOMAIN (UNP RESIDUES 106-224);
COMPND   5 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE, 25
COMPND   6 KDA FKBP, FKBP-25, RAPAMYCIN-SELECTIVE 25 KDA IMMUNOPHILIN;
COMPND   7 EC: 5.2.1.8;
COMPND   8 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE   3 ORGANISM_COMMON: MOUSE;
SOURCE   4 ORGANISM_TAXID: 10090;
SOURCE   5 GENE: FKBP25, FKBP3;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-2
KEYWDS    FKPB PPIASE RAPAMYCIN, ISOMERASE, NUCLEUS, PHOSPHOPROTEIN, ROTAMASE,
KEYWDS   2 ISOMERASE-INHIBITOR COMPLEX
EXPDTA    X-RAY DIFFRACTION
AUTHOR    E.A.STURA,A.GALAT
REVDAT   3   20-AUG-14 3KZ7    1       JRNL
REVDAT   2   18-JUN-14 3KZ7    1       JRNL   VERSN
REVDAT   1   15-DEC-10 3KZ7    0
JRNL        AUTH   A.GALAT,R.THAI,E.A.STURA
JRNL        TITL   DIVERSIFIED TARGETS OF FKBP25 AND ITS COMPLEX WITH
JRNL        TITL 2 RAPAMYCIN.
JRNL        REF    INT.J.BIOL.MACROMOL.          V.  69   344 2014
JRNL        REFN                   ISSN 0141-8130
JRNL        PMID   24879919
JRNL        DOI    10.1016/J.IJBIOMAC.2014.05.060
REMARK   2
REMARK   2 RESOLUTION.    1.95 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE)
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT 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) : 1.95
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 38.30
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.930
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.5
REMARK   3   NUMBER OF REFLECTIONS             : 14836
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.177
REMARK   3   R VALUE            (WORKING SET) : 0.175
REMARK   3   FREE R VALUE                     : 0.222
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.990
REMARK   3   FREE R VALUE TEST SET COUNT      : 740
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 38.3106 -  3.3340    0.98     2925   146  0.1653 0.1920
REMARK   3     2  3.3340 -  2.6465    1.00     2832   146  0.1770 0.2298
REMARK   3     3  2.6465 -  2.3120    1.00     2810   138  0.1903 0.2660
REMARK   3     4  2.3120 -  2.1006    1.00     2774   149  0.1763 0.2455
REMARK   3     5  2.1006 -  1.9501    1.00     2755   161  0.1845 0.2191
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
REMARK   3   SOLVENT RADIUS     : 1.11
REMARK   3   SHRINKAGE RADIUS   : 0.90
REMARK   3   K_SOL              : 0.37
REMARK   3   B_SOL              : 64.66
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.070
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 25.60
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.99160
REMARK   3    B22 (A**2) : -0.99160
REMARK   3    B33 (A**2) : 1.98320
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      :  0.006           1057
REMARK   3   ANGLE     :  1.075           1439
REMARK   3   CHIRALITY :  0.073            162
REMARK   3   PLANARITY :  0.004            180
REMARK   3   DIHEDRAL  : 16.972            430
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 : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3KZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-09.
REMARK 100 THE RCSB ID CODE IS RCSB056631.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 29-APR-05
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID14-1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.934
REMARK 200  MONOCHROMATOR                  : DIAMOND (111)
REMARK 200  OPTICS                         : HORIZONTALLY BENT GE(220)
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          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 23011
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.680
REMARK 200  RESOLUTION RANGE LOW       (A) : 68.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 1.200
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8
REMARK 200  DATA REDUNDANCY                : 14.000
REMARK 200  R MERGE                    (I) : 0.06800
REMARK 200  R SYM                      (I) : 0.06800
REMARK 200   FOR THE DATA SET  : 6.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.88
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 14.00
REMARK 200  R MERGE FOR SHELL          (I) : 0.12000
REMARK 200  R SYM FOR SHELL            (I) : 0.12000
REMARK 200   FOR SHELL         : 12.800
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: 1PBK
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 66.44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 120MM NA
REMARK 280  CITRATE, PH 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4
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       26.54500
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       42.82450
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       42.82450
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       13.27250
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       42.82450
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       42.82450
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       39.81750
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       42.82450
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       42.82450
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       13.27250
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       42.82450
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       42.82450
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       39.81750
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       26.54500
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480   M RES C SSEQI ATOMS
REMARK 480     GLU A  106   CD
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   C51  RAP A   225     O    HOH A    31              1.90
REMARK 500   CG   LYS A   154     ND2  ASN A   158              2.17
REMARK 500   OE1  GLU A   177     O    HOH A    65              2.19
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    SER A 153       -8.18     77.03
REMARK 500    ALA A 197     -111.60   -124.33
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 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A 286        DISTANCE =  7.65 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RAP A 225
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1PBK   RELATED DB: PDB
REMARK 900 HUMAN FKBP25 RAPAMYCIN COMPLEX
DBREF  3KZ7 A  106   224  UNP    Q62446   FKBP3_MOUSE    106    224
SEQRES   1 A  119  GLU GLY PRO PRO LYS TYR THR LYS SER ILE LEU LYS LYS
SEQRES   2 A  119  GLY ASP LYS THR ASN PHE PRO LYS LYS GLY ASP VAL VAL
SEQRES   3 A  119  HIS CYS TRP TYR THR GLY THR LEU PRO ASP GLY THR VAL
SEQRES   4 A  119  PHE ASP THR ASN ILE GLN THR SER SER LYS LYS LYS LYS
SEQRES   5 A  119  ASN ALA LYS PRO LEU SER PHE LYS VAL GLY VAL GLY LYS
SEQRES   6 A  119  VAL ILE ARG GLY TRP ASP GLU ALA LEU LEU THR MET SER
SEQRES   7 A  119  LYS GLY GLU LYS ALA ARG LEU GLU ILE GLU PRO GLU TRP
SEQRES   8 A  119  ALA TYR GLY LYS LYS GLY GLN PRO ASP ALA LYS ILE PRO
SEQRES   9 A  119  PRO ASN THR LYS LEU ILE PHE GLU VAL GLU LEU VAL ASP
SEQRES  10 A  119  ILE ASP
HET    RAP  A 225      65
HETNAM     RAP RAPAMYCIN IMMUNOSUPPRESSANT DRUG
FORMUL   2  RAP    C51 H79 N O13
FORMUL   3  HOH   *171(H2 O)
HELIX    1   1 ILE A  172  LEU A  180  1                                   9
HELIX    2   2 PRO A  194  ALA A  197  5                                   4
HELIX    3   3 GLN A  203  LYS A  207  5                                   5
SHEET    1   A 5 TYR A 111  LYS A 117  0
SHEET    2   A 5 LYS A 187  ILE A 192 -1  O  ARG A 189   N  SER A 114
SHEET    3   A 5 LEU A 214  ASP A 224 -1  O  PHE A 216   N  LEU A 190
SHEET    4   A 5 VAL A 130  THR A 138 -1  N  THR A 138   O  ILE A 215
SHEET    5   A 5 VAL A 144  THR A 147 -1  O  ASP A 146   N  GLY A 137
SHEET    1   B 5 TYR A 111  LYS A 117  0
SHEET    2   B 5 LYS A 187  ILE A 192 -1  O  ARG A 189   N  SER A 114
SHEET    3   B 5 LEU A 214  ASP A 224 -1  O  PHE A 216   N  LEU A 190
SHEET    4   B 5 VAL A 130  THR A 138 -1  N  THR A 138   O  ILE A 215
SHEET    5   B 5 LEU A 162  LYS A 165 -1  O  PHE A 164   N  VAL A 131
CISPEP   1 GLY A  107    PRO A  108          0         0.60
SITE     1 AC1 15 HOH A  31  HOH A  96  TYR A 135  PHE A 145
SITE     2 AC1 15 ASP A 146  LEU A 162  GLY A 169  LYS A 170
SITE     3 AC1 15 VAL A 171  ILE A 172  TRP A 175  TYR A 198
SITE     4 AC1 15 GLN A 203  PHE A 216  HOH A 244
CRYST1   85.649   85.649   53.090  90.00  90.00  90.00 P 41 21 2     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      0.011676  0.000000  0.000000        0.00000
SCALE2      0.000000  0.011676  0.000000        0.00000
SCALE3      0.000000  0.000000  0.018836        0.00000
      
PROCHECK
Go to PROCHECK summary
 References