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PDBsum entry 1m9e

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Top Page protein Protein-protein interface(s) links
Isomerase/viral protein PDB id
1m9e
Jmol
Contents
Protein chains
164 a.a. *
146 a.a. *
135 a.a. *
Waters ×380
* Residue conservation analysis
HEADER    ISOMERASE/VIRAL PROTEIN                 28-JUL-02   1M9E
TITLE     X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-
TITLE    2 TERMINAL DOMAIN (1-146) M-TYPE H87A COMPLEX.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CYCLOPHILIN A;
COMPND   3 CHAIN: A, B;
COMPND   4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A, PPIASE,
COMPND   5 ROTAMASE, CYCLOSPORIN A-BINDING PROTEIN;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: HIV-1 CAPSID;
COMPND  10 CHAIN: C, D;
COMPND  11 FRAGMENT: N-TERMINAL DOMAIN;
COMPND  12 ENGINEERED: YES;
COMPND  13 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
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: PET3A;
SOURCE  10 MOL_ID: 2;
SOURCE  11 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE  12 ORGANISM_TAXID: 11676;
SOURCE  13 GENE: CA;
SOURCE  14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE  15 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE  16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE  17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  18 EXPRESSION_SYSTEM_PLASMID: PET11A
KEYWDS    CAPSID, HIV-1, CYCLOPHILIN A, ISOMERASE, ROTAMASE,
KEYWDS   2 ISOMERASE/VIRAL PROTEIN COMPLEX
EXPDTA    X-RAY DIFFRACTION
AUTHOR    B.R.HOWARD,F.F.VAJDOS,S.LI,W.I.SUNDQUIST,C.P.HILL
REVDAT   2   24-FEB-09 1M9E    1       VERSN
REVDAT   1   27-MAY-03 1M9E    0
JRNL        AUTH   B.R.HOWARD,F.F.VAJDOS,S.LI,W.I.SUNDQUIST,C.P.HILL
JRNL        TITL   STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM
JRNL        TITL 2 OF CYCLOPHILIN A
JRNL        REF    NAT.STRUCT.BIOL.              V.  10   475 2003
JRNL        REFN                   ISSN 1072-8368
JRNL        PMID   12730686
JRNL        DOI    10.1038/NSB927
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.72 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5
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) : 1.72
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.73
REMARK   3   DATA CUTOFF            (SIGMA(F)) : -3.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 77.7
REMARK   3   NUMBER OF REFLECTIONS             : 41047
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) : 0.178
REMARK   3   R VALUE            (WORKING SET) : 0.173
REMARK   3   FREE R VALUE                     : 0.226
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 4623
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) : 1.72
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.76
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1019
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 31.00
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2910
REMARK   3   BIN FREE R VALUE SET COUNT          : 102
REMARK   3   BIN FREE R VALUE                    : 0.3950
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 4677
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 380
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 30.30
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 20.18
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.67000
REMARK   3    B22 (A**2) : 1.29000
REMARK   3    B33 (A**2) : -0.75000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : -0.35000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.165
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.154
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.147
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.720
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.953
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  4786 ; 0.018 ; 0.021
REMARK   3   BOND LENGTHS OTHERS               (A):  4287 ; 0.000 ; 0.020
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  6461 ; 3.034 ; 1.941
REMARK   3   BOND ANGLES OTHERS          (DEGREES): 10027 ; 1.218 ; 3.000
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   603 ; 6.081 ; 3.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   884 ;19.417 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   691 ; 0.181 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  5361 ; 0.017 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):   949 ; 0.008 ; 0.020
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1136 ; 0.241 ; 0.300
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  4512 ; 0.214 ; 0.300
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   745 ; 0.186 ; 0.500
REMARK   3   H-BOND (X...Y) OTHERS             (A):     4 ; 0.068 ; 0.500
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):    17 ; 0.300 ; 0.300
REMARK   3   SYMMETRY VDW OTHERS               (A):    80 ; 0.260 ; 0.300
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    42 ; 0.229 ; 0.500
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):  3003 ; 2.875 ; 2.000
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  4825 ; 3.998 ; 3.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1783 ; 3.195 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1636 ; 4.760 ; 3.000
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 : BABINET MODEL WITH MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3  RIDING POSITIONS BUT NOT OUTPUT TO THE ATOMIC COORDINATE FILE.
REMARK   4
REMARK   4 1M9E COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-02.
REMARK 100 THE RCSB ID CODE IS RCSB016760.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 12-APR-98
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 8.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SSRL
REMARK 200  BEAMLINE                       : BL1-5
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.07
REMARK 200  MONOCHROMATOR                  : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200                                   SI(111)
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 41047
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.720
REMARK 200  RESOLUTION RANGE LOW       (A) : 26.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 78.0
REMARK 200  DATA REDUNDANCY                : 4.600
REMARK 200  R MERGE                    (I) : 0.05600
REMARK 200  R SYM                      (I) : 0.05600
REMARK 200   FOR THE DATA SET  : 9.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.82
REMARK 200  COMPLETENESS FOR SHELL     (%) : 31.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.70
REMARK 200  R MERGE FOR SHELL          (I) : 0.30400
REMARK 200  R SYM FOR SHELL            (I) : 0.30400
REMARK 200   FOR SHELL         : 2.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: PDB ENTRY 1AK4
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 36.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, BICINE, LICL, TRIS, BETA-
REMARK 280  MERCAPTOETHANOL, PH 8.0, VAPOR DIFFUSION, SITTING DROP,
REMARK 280  TEMPERATURE 294K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       55.49450
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC
REMARK 300 UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350
REMARK 300 FOR INFORMATION ON GENERATING THE BIOLOGICAL
REMARK 300 MOLECULE(S).
REMARK 300 COMPLEX "A" CONSISTS OF CHAINS B AND C;
REMARK 300 COMPLEX "B" CONSISTS OF CHAINS A AND D.
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, D
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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     VAL B     2
REMARK 465     PRO D     1
REMARK 465     ILE D     2
REMARK 465     VAL D     3
REMARK 465     GLN D     4
REMARK 465     ASN D     5
REMARK 465     LEU D     6
REMARK 465     GLN D     7
REMARK 465     GLY D     8
REMARK 465     GLN D     9
REMARK 465     MET D    10
REMARK 465     VAL D    11
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   ND2  ASN C     5     OE1  GLN C     7              1.93
REMARK 500   O    HOH B   242     O    HOH B   249              2.15
REMARK 500   NZ   LYS A   125     O    HOH A   240              2.18
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   OE1  GLU C    29     NZ   LYS D    30     1455     1.97
REMARK 500   O    HOH A   286     O    HOH C   190     2756     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    VAL A   6   CA  -  CB  -  CG2 ANGL. DEV. = -10.4 DEGREES
REMARK 500    ASP A   9   CB  -  CG  -  OD1 ANGL. DEV. =   8.5 DEGREES
REMARK 500    ARG A  19   NE  -  CZ  -  NH2 ANGL. DEV. =  -8.1 DEGREES
REMARK 500    ARG A  37   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 DEGREES
REMARK 500    ARG A  55   NE  -  CZ  -  NH1 ANGL. DEV. =   4.3 DEGREES
REMARK 500    ARG A  55   NE  -  CZ  -  NH2 ANGL. DEV. =  -7.0 DEGREES
REMARK 500    LYS A 131   CD  -  CE  -  NZ  ANGL. DEV. = -15.3 DEGREES
REMARK 500    ASP A 160   CB  -  CG  -  OD1 ANGL. DEV. =   8.1 DEGREES
REMARK 500    ASP A 160   CB  -  CG  -  OD2 ANGL. DEV. =  -6.2 DEGREES
REMARK 500    ARG B  19   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.7 DEGREES
REMARK 500    LEU B  24   CB  -  CG  -  CD1 ANGL. DEV. = -12.6 DEGREES
REMARK 500    ASP B  27   CB  -  CG  -  OD2 ANGL. DEV. =   5.8 DEGREES
REMARK 500    ARG B  37   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES
REMARK 500    ARG B  37   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.2 DEGREES
REMARK 500    ARG B  55   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.8 DEGREES
REMARK 500    ARG B  69   NE  -  CZ  -  NH1 ANGL. DEV. =   4.1 DEGREES
REMARK 500    THR B  93   OG1 -  CB  -  CG2 ANGL. DEV. = -16.6 DEGREES
REMARK 500    ASP B 123   CB  -  CG  -  OD1 ANGL. DEV. =   6.4 DEGREES
REMARK 500    MET B 136   CG  -  SD  -  CE  ANGL. DEV. = -13.9 DEGREES
REMARK 500    ASP B 160   CB  -  CG  -  OD1 ANGL. DEV. =   5.6 DEGREES
REMARK 500    ILE C   2   CA  -  CB  -  CG1 ANGL. DEV. = -11.5 DEGREES
REMARK 500    ARG C  18   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.4 DEGREES
REMARK 500    ASP C  81   CB  -  CG  -  OD1 ANGL. DEV. =   5.8 DEGREES
REMARK 500    PRO C  85   N   -  CD  -  CG  ANGL. DEV. = -11.0 DEGREES
REMARK 500    ARG C 100   NE  -  CZ  -  NH2 ANGL. DEV. =   4.2 DEGREES
REMARK 500    ASP C 103   CB  -  CG  -  OD1 ANGL. DEV. =   5.8 DEGREES
REMARK 500    LEU C 111   CB  -  CG  -  CD2 ANGL. DEV. = -12.1 DEGREES
REMARK 500    GLU C 128   OE1 -  CD  -  OE2 ANGL. DEV. =  -9.0 DEGREES
REMARK 500    ARG C 143   NE  -  CZ  -  NH1 ANGL. DEV. =   3.4 DEGREES
REMARK 500    ARG C 143   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.5 DEGREES
REMARK 500    SER C 146   CA  -  C   -  O   ANGL. DEV. = -13.7 DEGREES
REMARK 500    HIS D  12   N   -  CA  -  C   ANGL. DEV. =  20.2 DEGREES
REMARK 500    ILE D  15   CB  -  CA  -  C   ANGL. DEV. = -12.4 DEGREES
REMARK 500    PHE D  32   CB  -  CA  -  C   ANGL. DEV. =  17.4 DEGREES
REMARK 500    PHE D  32   N   -  CA  -  CB  ANGL. DEV. = -11.4 DEGREES
REMARK 500    MET D  39   CG  -  SD  -  CE  ANGL. DEV. =  16.3 DEGREES
REMARK 500    ASP D  81   CB  -  CG  -  OD2 ANGL. DEV. =   6.1 DEGREES
REMARK 500    ARG D 100   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES
REMARK 500    ARG D 143   CG  -  CD  -  NE  ANGL. DEV. =  16.6 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    LEU A  17      -63.94   -109.06
REMARK 500    PHE A  60      -77.03   -129.80
REMARK 500    ASN A 102      155.04     53.57
REMARK 500    LYS A 133      -69.98   -104.85
REMARK 500    PHE B  60      -70.11   -138.71
REMARK 500    ASN B  71       15.96   -158.29
REMARK 500    ALA C  31     -141.06     54.28
REMARK 500    PHE C  32       53.11   -112.89
REMARK 500    LYS D  30       39.44    -99.99
REMARK 500    PHE D  32       32.88     84.07
REMARK 500    LEU D 111      -60.00    -29.50
REMARK 500    HIS D 120      158.94    -45.50
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 ALA C   88     GLY C   89                  144.56
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        ANGLE
REMARK 500    ALA C  88        -10.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AK4   RELATED DB: PDB
REMARK 900 HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF
REMARK 900 HIV-1 CAPSID (1-151)
REMARK 900 RELATED ID: 1M96   RELATED DB: PDB
REMARK 900 HIV-1 CA 1-146 A92E CRYSTAL STRUCTURE
REMARK 900 RELATED ID: 1M9C   RELATED DB: PDB
REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-
REMARK 900 TERMINAL DOMAIN (1-146) M-TYPE COMPLEX.
REMARK 900 RELATED ID: 1M9D   RELATED DB: PDB
REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-
REMARK 900 TERMINAL DOMAIN (1-146) O-TYPE CHIMERA COMPLEX.
REMARK 900 RELATED ID: 1M9F   RELATED DB: PDB
REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-
REMARK 900 TERMINAL DOMAIN (1-146) M-TYPE H87A, A88M COMPLEX.
REMARK 900 RELATED ID: 1M9X   RELATED DB: PDB
REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-
REMARK 900 TERMINAL DOMAIN (1-146) M-TYPE H87A,A88M,G89A COMPLEX.
REMARK 900 RELATED ID: 1M9Y   RELATED DB: PDB
REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-
REMARK 900 TERMINAL DOMAIN (1-146) M-TYPE H87A,G89A COMPLEX.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 ACCORDING TO THE AUTHORS, THIS APPARENT CONFLICT IS
REMARK 999 DUE TO THE USE OF HIV-1 STRAIN NL4-3 WHICH HAS A
REMARK 999 HISTIDINE AT RESIDUE 120.
DBREF  1M9E A    1   164  UNP    P62937   PPIA_HUMAN       1    163
DBREF  1M9E B    1   164  UNP    P62937   PPIA_HUMAN       1    163
DBREF  1M9E C    1   146  UNP    Q72497   Q72497_9HIV1   133    278
DBREF  1M9E D    1   146  UNP    Q72497   Q72497_9HIV1   133    278
SEQADV 1M9E ALA C   87  UNP  Q72497    HIS   219 ENGINEERED
SEQADV 1M9E HIS C  120  UNP  Q72497    ASN   252 SEE REMARK 999
SEQADV 1M9E ALA D   87  UNP  Q72497    HIS   219 ENGINEERED
SEQADV 1M9E HIS D  120  UNP  Q72497    ASN   252 SEE REMARK 999
SEQRES   1 A  164  MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP
SEQRES   2 A  164  GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA
SEQRES   3 A  164  ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU
SEQRES   4 A  164  SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS
SEQRES   5 A  164  PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY
SEQRES   6 A  164  ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE
SEQRES   7 A  164  TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS
SEQRES   8 A  164  HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY
SEQRES   9 A  164  PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA
SEQRES  10 A  164  LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY
SEQRES  11 A  164  LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU
SEQRES  12 A  164  ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE
SEQRES  13 A  164  THR ILE ALA ASP CYS GLY GLN LEU
SEQRES   1 B  164  MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP
SEQRES   2 B  164  GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA
SEQRES   3 B  164  ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU
SEQRES   4 B  164  SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS
SEQRES   5 B  164  PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY
SEQRES   6 B  164  ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE
SEQRES   7 B  164  TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS
SEQRES   8 B  164  HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY
SEQRES   9 B  164  PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA
SEQRES  10 B  164  LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY
SEQRES  11 B  164  LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU
SEQRES  12 B  164  ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE
SEQRES  13 B  164  THR ILE ALA ASP CYS GLY GLN LEU
SEQRES   1 C  146  PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN
SEQRES   2 C  146  ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL
SEQRES   3 C  146  VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET
SEQRES   4 C  146  PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU
SEQRES   5 C  146  ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA
SEQRES   6 C  146  MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA
SEQRES   7 C  146  GLU TRP ASP ARG LEU HIS PRO VAL ALA ALA GLY PRO ILE
SEQRES   8 C  146  ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE
SEQRES   9 C  146  ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP
SEQRES  10 C  146  MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR
SEQRES  11 C  146  LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG
SEQRES  12 C  146  MET TYR SER
SEQRES   1 D  146  PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN
SEQRES   2 D  146  ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL
SEQRES   3 D  146  VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET
SEQRES   4 D  146  PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU
SEQRES   5 D  146  ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA
SEQRES   6 D  146  MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA
SEQRES   7 D  146  GLU TRP ASP ARG LEU HIS PRO VAL ALA ALA GLY PRO ILE
SEQRES   8 D  146  ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE
SEQRES   9 D  146  ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP
SEQRES  10 D  146  MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR
SEQRES  11 D  146  LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG
SEQRES  12 D  146  MET TYR SER
FORMUL   5  HOH   *380(H2 O)
HELIX    1   1 VAL A   29  GLY A   42  1                                  14
HELIX    2   2 THR A  119  ASP A  123  5                                   5
HELIX    3   3 GLY A  135  ARG A  144  1                                  10
HELIX    4   4 VAL B   29  GLY B   42  1                                  14
HELIX    5   5 THR B  119  ASP B  123  5                                   5
HELIX    6   6 GLY B  135  GLU B  143  1                                   9
HELIX    7   7 ARG B  144  GLY B  146  5                                   3
HELIX    8   8 SER C   16  ALA C   31  1                                  16
HELIX    9   9 GLU C   35  SER C   44  1                                  10
HELIX   10  10 THR C   48  THR C   58  1                                  11
HELIX   11  11 HIS C   62  HIS C   84  1                                  23
HELIX   12  12 ARG C  100  ALA C  105  1                                   6
HELIX   13  13 THR C  110  HIS C  120  1                                  11
HELIX   14  14 PRO C  125  ARG C  143  1                                  19
HELIX   15  15 SER D   16  LYS D   30  1                                  15
HELIX   16  16 GLU D   35  SER D   44  1                                  10
HELIX   17  17 THR D   48  THR D   58  1                                  11
HELIX   18  18 HIS D   62  LEU D   83  1                                  22
HELIX   19  19 ARG D  100  ALA D  105  1                                   6
HELIX   20  20 THR D  110  HIS D  120  1                                  11
HELIX   21  21 PRO D  125  SER D  146  1                                  22
SHEET    1   A 8 ARG A  55  ILE A  57  0
SHEET    2   A 8 MET A  61  GLY A  64 -1  O  GLN A  63   N  ARG A  55
SHEET    3   A 8 PHE A 112  CYS A 115 -1  O  ILE A 114   N  CYS A  62
SHEET    4   A 8 ILE A  97  MET A 100 -1  N  SER A  99   O  PHE A 113
SHEET    5   A 8 VAL A 128  VAL A 132 -1  O  PHE A 129   N  LEU A  98
SHEET    6   A 8 GLU A  15  LEU A  24 -1  N  GLU A  23   O  LYS A 131
SHEET    7   A 8 THR A   5  VAL A  12 -1  N  ILE A  10   O  LEU A  17
SHEET    8   A 8 ILE A 156  LEU A 164 -1  O  ASP A 160   N  ASP A   9
SHEET    1   B 8 PHE B  53  ILE B  57  0
SHEET    2   B 8 MET B  61  GLY B  64 -1  O  GLN B  63   N  ARG B  55
SHEET    3   B 8 PHE B 112  CYS B 115 -1  O  ILE B 114   N  CYS B  62
SHEET    4   B 8 ILE B  97  MET B 100 -1  N  SER B  99   O  PHE B 113
SHEET    5   B 8 VAL B 128  GLU B 134 -1  O  GLY B 130   N  LEU B  98
SHEET    6   B 8 GLU B  15  LEU B  24 -1  N  SER B  21   O  LYS B 133
SHEET    7   B 8 THR B   5  VAL B  12 -1  N  ILE B  10   O  GLY B  18
SHEET    8   B 8 ILE B 156  GLN B 163 -1  O  ASP B 160   N  ASP B   9
SHEET    1   C 2 ILE C   2  GLN C   4  0
SHEET    2   C 2 MET C  10  HIS C  12 -1  O  VAL C  11   N  VAL C   3
CISPEP   1 ASN C  121    PRO C  122          0         0.23
CISPEP   2 ASN D  121    PRO D  122          0        -2.40
CRYST1   38.289  110.989   67.685  90.00 101.02  90.00 P 1 21 1      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      0.026117  0.000000  0.005085        0.00000
SCALE2      0.000000  0.009010  0.000000        0.00000
SCALE3      0.000000  0.000000  0.015052        0.00000
      
PROCHECK
Go to PROCHECK summary
 References