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PDBsum entry 2d9f

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Isomerase PDB id
2d9f
Jmol
Contents
Protein chain
135 a.a.
HEADER    ISOMERASE                               09-DEC-05   2D9F
TITLE     SOLUTION STRUCTURE OF RUH-047, AN FKBP DOMAIN FROM HUMAN
TITLE    2 CDNA
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FK506-BINDING PROTEIN 8 VARIANT;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: RESIDUES 8-129;
COMPND   5 SYNONYM: FK506-BINDING DOMAIN, FKBP;
COMPND   6 ENGINEERED: 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_VECTOR_TYPE: PLASMID;
SOURCE   6 EXPRESSION_SYSTEM_PLASMID: P040614-07;
SOURCE   7 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS    FKBP, FK506 BINDING PROTEIN, RAPAMYCIN, STRUCTURAL GENOMICS,
KEYWDS   2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND
KEYWDS   3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS
KEYWDS   4 INITIATIVE, RSGI, ISOMERASE
EXPDTA    SOLUTION NMR
NUMMDL    20
AUTHOR    A.Z.M.RUHUL MOMEN,H.HIROTA,S.KOSHIBA,T.KIGAWA,S.YOKOYAMA,
AUTHOR   2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT   2   24-FEB-09 2D9F    1       VERSN
REVDAT   1   09-JUN-06 2D9F    0
JRNL        AUTH   A.Z.M.RUHUL MOMEN,H.HIROTA,S.KOSHIBA,T.KIGAWA,
JRNL        AUTH 2 S.YOKOYAMA
JRNL        TITL   SOLUTION STRUCTURE OF RUH-047, AN FKBP DOMAIN FROM
JRNL        TITL 2 HUMAN CDNA
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CYANA 2.0.17
REMARK   3   AUTHORS     : GUNTERT, P.
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2D9F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-05.
REMARK 100 THE RCSB ID CODE IS RCSB025150.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 298
REMARK 210  PH                             : 7.0
REMARK 210  IONIC STRENGTH                 : 120MM NACL
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : 1.01MM DOMAIN U-15N, 13C;
REMARK 210                                   20MM D-TRIS-HCL (PH7.0); 100MM
REMARK 210                                   NACL; 1MM D-DTT; 0.02% NAN3;
REMARK 210                                   90%H2O, 10%D2O
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY, 3D_
REMARK 210                                   15N-SEPARATED_NOESY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ
REMARK 210  SPECTROMETER MODEL             : AVANCE
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : XWINNMR 3.6, NMRPIPE
REMARK 210                                   20031121, NMRVIEW 5.04, KUJIRA
REMARK 210                                   0.9295
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA  : TARGET FUNCTION,STRUCTURES
REMARK 210                                   WITH THE LOWEST ENERGY,
REMARK 210                                   STRUCTURES WITH THE LEAST
REMARK 210                                   RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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  1 TRP A  10      161.20    -40.68
REMARK 500  1 LEU A  18      -71.02    -60.08
REMARK 500  1 PRO A  34     -170.09    -69.76
REMARK 500  1 GLU A  59       73.51   -112.39
REMARK 500  1 PRO A  78        2.95    -69.76
REMARK 500  1 CYS A  95      -71.22    -77.19
REMARK 500  1 PRO A  98        2.81    -69.78
REMARK 500  1 ARG A 102      -69.79   -107.14
REMARK 500  1 HIS A 109       26.40     48.43
REMARK 500  1 ALA A 111      159.44    -46.56
REMARK 500  1 LYS A 119      -61.03    -93.74
REMARK 500  1 MET A 129       51.71     34.76
REMARK 500  2 GLU A   8       40.30   -107.61
REMARK 500  2 ARG A  33      139.84    -37.78
REMARK 500  2 PRO A  34     -170.20    -69.75
REMARK 500  2 PRO A  78        3.13    -69.78
REMARK 500  2 ARG A 102      -65.01   -105.59
REMARK 500  2 HIS A 109       27.49     43.52
REMARK 500  2 ALA A 111      160.50    -48.39
REMARK 500  2 SER A 130      173.40    -53.34
REMARK 500  3 SER A   2      107.06    -41.76
REMARK 500  3 LEU A  18      -70.27    -62.00
REMARK 500  3 SER A  32      136.27   -171.71
REMARK 500  3 ARG A  33      137.42    -39.22
REMARK 500  3 PRO A  34     -164.04    -69.73
REMARK 500  3 GLU A  59       74.06   -110.17
REMARK 500  3 PRO A  78        4.28    -69.76
REMARK 500  3 SER A  92      -36.38    -36.71
REMARK 500  3 CYS A  95      -72.54    -78.82
REMARK 500  3 SER A 103      105.38   -160.13
REMARK 500  3 HIS A 109       25.24     45.45
REMARK 500  3 ALA A 111      159.09    -46.66
REMARK 500  3 GLU A 128       77.50    -65.29
REMARK 500  4 LEU A  18      -70.16    -64.79
REMARK 500  4 SER A  31      170.19    -57.88
REMARK 500  4 PRO A  34     -172.89    -69.80
REMARK 500  4 PRO A  78        4.90    -69.79
REMARK 500  4 CYS A  95      -73.42    -78.94
REMARK 500  4 PRO A  98        2.77    -69.73
REMARK 500  4 ARG A 102      -65.02   -105.79
REMARK 500  4 ALA A 111      160.34    -43.06
REMARK 500  4 LEU A 127       96.18    -57.46
REMARK 500  4 SER A 133      163.13    -43.52
REMARK 500  5 SER A   2      165.79    -48.79
REMARK 500  5 GLU A   8       31.83    -93.73
REMARK 500  5 SER A  31      170.91    -52.40
REMARK 500  5 PRO A  34     -165.17    -69.75
REMARK 500  5 PRO A  78        3.25    -69.76
REMARK 500  5 CYS A  95      -71.42    -74.46
REMARK 500  5 PRO A  98        1.33    -69.80
REMARK 500  5 ARG A 102      -70.01   -114.36
REMARK 500  5 ALA A 111      156.73    -49.64
REMARK 500  5 LYS A 119      -61.58    -91.60
REMARK 500  6 SER A   2      142.67    -35.53
REMARK 500  6 GLU A   9     -174.99    -69.88
REMARK 500  6 TRP A  10      163.82    -43.16
REMARK 500  6 PRO A  34     -169.93    -69.80
REMARK 500  6 PRO A  78        3.45    -69.71
REMARK 500  6 VAL A  82      108.25    -59.60
REMARK 500  6 CYS A  95      -72.62    -79.80
REMARK 500  6 PRO A  98        0.96    -69.71
REMARK 500  6 LYS A 119      -67.65    -91.36
REMARK 500  7 GLU A   8       51.16    -94.75
REMARK 500  7 GLU A   9      -37.11   -133.15
REMARK 500  7 SER A  32      136.22   -171.28
REMARK 500  7 ARG A  33      140.39    -38.86
REMARK 500  7 PRO A  34     -168.95    -69.75
REMARK 500  7 PRO A  78        3.33    -69.82
REMARK 500  7 TYR A  96      -31.10   -130.09
REMARK 500  7 SER A 103      110.46    -29.78
REMARK 500  7 HIS A 109       29.68     41.19
REMARK 500  7 LYS A 119      -71.41    -91.02
REMARK 500  7 GLU A 128       36.99     36.25
REMARK 500  7 MET A 129       39.83    -83.74
REMARK 500  8 SER A   2      165.44    -44.80
REMARK 500  8 SER A   3      111.08   -169.42
REMARK 500  8 GLU A   8       44.84    -98.99
REMARK 500  8 TRP A  10      151.50    -34.87
REMARK 500  8 SER A  31      171.29    -58.44
REMARK 500  8 SER A  32      143.87   -170.48
REMARK 500  8 ARG A  33      140.29    -36.75
REMARK 500  8 PRO A  34     -172.44    -69.75
REMARK 500  8 GLN A  55      146.40   -171.14
REMARK 500  8 CYS A  67       37.89     36.69
REMARK 500  8 PRO A  78        2.39    -69.73
REMARK 500  8 ARG A 102      -66.00   -103.42
REMARK 500  8 LYS A 119      -62.12    -96.76
REMARK 500  8 ASP A 126       43.08    -95.20
REMARK 500  8 MET A 129       41.80     72.12
REMARK 500  9 ARG A  33      137.34    -39.33
REMARK 500  9 PRO A  34     -168.32    -69.76
REMARK 500  9 PRO A  78        2.89    -69.74
REMARK 500  9 SER A 103      112.69   -160.22
REMARK 500  9 HIS A 109       28.76     47.78
REMARK 500  9 LYS A 119      -68.66    -91.05
REMARK 500  9 SER A 130       44.29    -85.28
REMARK 500 10 SER A   2      -56.94   -133.97
REMARK 500 10 GLU A   9       26.55     41.18
REMARK 500 10 PRO A  29        3.48    -69.79
REMARK 500 10 SER A  31      176.73    -53.51
REMARK 500 10 PRO A  34     -170.89    -69.80
REMARK 500 10 PRO A  78        3.46    -69.75
REMARK 500 10 CYS A  95      -70.80    -72.57
REMARK 500 10 SER A 103      108.20    -27.32
REMARK 500 10 LYS A 119      -60.17    -95.08
REMARK 500 11 SER A   2      -43.50   -131.36
REMARK 500 11 GLU A   8       49.70    -98.83
REMARK 500 11 THR A  23      102.83    -53.58
REMARK 500 11 PRO A  29        1.09    -69.75
REMARK 500 11 ARG A  33      138.13    -38.28
REMARK 500 11 PRO A  34     -172.65    -69.79
REMARK 500 11 GLU A  59       75.72   -109.06
REMARK 500 11 LEU A  64      139.44    -38.25
REMARK 500 11 PRO A  78        3.64    -69.71
REMARK 500 11 SER A  92      -35.68    -34.82
REMARK 500 11 PRO A  98        0.94    -69.68
REMARK 500 11 SER A 103      110.98    -30.12
REMARK 500 12 PRO A  34     -166.89    -69.76
REMARK 500 12 GLU A  59       75.26   -108.77
REMARK 500 12 PRO A  78        3.10    -69.77
REMARK 500 12 CYS A  95      -73.64    -75.74
REMARK 500 12 SER A 103      118.13   -160.26
REMARK 500 12 ALA A 111      160.64    -48.51
REMARK 500 12 SER A 130       40.29    -98.40
REMARK 500 13 SER A  31      170.46    -58.59
REMARK 500 13 PRO A  34     -163.81    -69.76
REMARK 500 13 GLU A  59       72.06   -112.08
REMARK 500 13 PRO A  78        4.10    -69.69
REMARK 500 13 VAL A  82      105.09    -59.22
REMARK 500 13 PRO A  98        1.72    -69.72
REMARK 500 13 SER A 103      112.58   -168.49
REMARK 500 14 THR A  23      103.51    -58.91
REMARK 500 14 SER A  31      169.47    -45.63
REMARK 500 14 PRO A  34     -168.83    -69.73
REMARK 500 14 PRO A  78        3.40    -69.79
REMARK 500 14 SER A  92      -38.18    -39.88
REMARK 500 14 TYR A  96      -34.18   -132.90
REMARK 500 14 PRO A  98        2.25    -69.81
REMARK 500 14 ARG A 102      -63.83   -102.97
REMARK 500 14 HIS A 109       29.29     48.87
REMARK 500 14 LYS A 119      -64.26    -94.59
REMARK 500 14 MET A 129      125.46   -172.97
REMARK 500 15 GLU A   8       40.11    -90.65
REMARK 500 15 SER A  31      166.18    -46.09
REMARK 500 15 ARG A  33      139.88    -38.97
REMARK 500 15 PRO A  34     -169.69    -69.75
REMARK 500 15 PRO A  78        4.75    -69.82
REMARK 500 15 SER A  92      -34.18    -39.77
REMARK 500 15 CYS A  95      -70.24    -79.62
REMARK 500 15 SER A 103      111.10    -30.42
REMARK 500 15 HIS A 109       27.69     48.10
REMARK 500 15 LYS A 119      -63.04    -91.52
REMARK 500 15 LEU A 127       89.43    -61.42
REMARK 500 15 GLU A 128      156.64    -38.41
REMARK 500 16 SER A   5      166.90    -49.19
REMARK 500 16 THR A  23      107.22    -56.55
REMARK 500 16 PRO A  34     -167.64    -69.75
REMARK 500 16 GLU A  59       79.56   -106.19
REMARK 500 16 PRO A  78        4.03    -69.75
REMARK 500 16 CYS A  95      -72.02    -77.47
REMARK 500 16 PRO A  98        4.02    -69.79
REMARK 500 16 SER A 103      109.05   -166.65
REMARK 500 16 SER A 133       44.80     37.56
REMARK 500 17 PRO A  34     -173.71    -69.77
REMARK 500 17 GLU A  59       74.27   -108.03
REMARK 500 17 PRO A  78        6.06    -69.76
REMARK 500 17 SER A  92      -35.35    -33.79
REMARK 500 17 CYS A  95      -72.85    -71.72
REMARK 500 17 SER A 103      110.10    -29.24
REMARK 500 17 ALA A 111      153.98    -46.55
REMARK 500 17 LYS A 119      -65.29    -90.10
REMARK 500 17 PRO A 132       85.17    -69.73
REMARK 500 18 SER A  32      137.46   -170.44
REMARK 500 18 PRO A  34     -164.02    -69.83
REMARK 500 18 PRO A  78        3.48    -69.74
REMARK 500 18 SER A  92      -33.98    -39.91
REMARK 500 18 CYS A  95      -72.96    -82.43
REMARK 500 18 PRO A  98        0.65    -69.77
REMARK 500 18 ARG A 102      -63.21   -107.55
REMARK 500 18 ALA A 111      161.50    -42.25
REMARK 500 18 LYS A 119      -66.98    -93.13
REMARK 500 18 MET A 129      106.58   -173.30
REMARK 500 18 PRO A 132       87.63    -69.75
REMARK 500 18 SER A 134       98.52    -65.96
REMARK 500 19 SER A   5      -60.48   -125.55
REMARK 500 19 TRP A  10      175.95    -48.88
REMARK 500 19 SER A  31      175.31    -55.38
REMARK 500 19 SER A  32      142.58   -170.53
REMARK 500 19 PRO A  34     -164.79    -69.78
REMARK 500 19 PRO A  78        1.41    -69.84
REMARK 500 19 SER A  92      -32.30    -35.69
REMARK 500 19 CYS A  95      -72.94    -76.05
REMARK 500 19 PRO A  98        2.14    -69.84
REMARK 500 19 SER A 103      111.04    -30.57
REMARK 500 19 HIS A 109       25.97     48.27
REMARK 500 19 ALA A 111      158.97    -45.93
REMARK 500 20 GLU A   8       44.63    -87.36
REMARK 500 20 TRP A  10      165.53    -42.43
REMARK 500 20 SER A  31      171.94    -55.76
REMARK 500 20 ARG A  33      139.74    -37.01
REMARK 500 20 PRO A  34     -168.84    -69.76
REMARK 500 20 GLU A  59       73.69   -113.66
REMARK 500 20 PRO A  78        3.12    -69.75
REMARK 500 20 PRO A  98        1.42    -69.77
REMARK 500 20 SER A 103      108.44   -171.16
REMARK 500 20 ALA A 111      159.11    -47.57
REMARK 500 20 MET A 129      -53.53   -129.56
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: HSS001001573.1   RELATED DB: TARGETDB
DBREF  2D9F A    8   129  GB     62897235 BAD96558        50    171
SEQADV 2D9F GLY A    1  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A    2  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A    3  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F GLY A    4  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A    5  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A    6  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F GLY A    7  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A  130  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F GLY A  131  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F PRO A  132  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A  133  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F SER A  134  GB   62897235            CLONING ARTIFACT
SEQADV 2D9F GLY A  135  GB   62897235            CLONING ARTIFACT
SEQRES   1 A  135  GLY SER SER GLY SER SER GLY GLU GLU TRP LEU ASP ILE
SEQRES   2 A  135  LEU GLY ASN GLY LEU LEU ARG LYS LYS THR LEU VAL PRO
SEQRES   3 A  135  GLY PRO PRO GLY SER SER ARG PRO VAL LYS GLY GLN VAL
SEQRES   4 A  135  VAL THR VAL HIS LEU GLN THR SER LEU GLU ASN GLY THR
SEQRES   5 A  135  ARG VAL GLN GLU GLU PRO GLU LEU VAL PHE THR LEU GLY
SEQRES   6 A  135  ASP CYS ASP VAL ILE GLN ALA LEU ASP LEU SER VAL PRO
SEQRES   7 A  135  LEU MET ASP VAL GLY GLU THR ALA MET VAL THR ALA ASP
SEQRES   8 A  135  SER LYS TYR CYS TYR GLY PRO GLN GLY SER ARG SER PRO
SEQRES   9 A  135  TYR ILE PRO PRO HIS ALA ALA LEU CYS LEU GLU VAL THR
SEQRES  10 A  135  LEU LYS THR ALA VAL ASP ARG PRO ASP LEU GLU MET SER
SEQRES  11 A  135  GLY PRO SER SER GLY
HELIX    1   1 SER A   76  MET A   80  5                                   5
HELIX    2   2 ASP A   91  TYR A   96  1                                   6
SHEET    1   A 6 LEU A  11  ASP A  12  0
SHEET    2   A 6 ARG A  20  VAL A  25 -1  O  LYS A  21   N  LEU A  11
SHEET    3   A 6 THR A  85  ALA A  90 -1  O  MET A  87   N  LYS A  22
SHEET    4   A 6 LEU A 112  VAL A 122 -1  O  LEU A 114   N  VAL A  88
SHEET    5   A 6 VAL A  39  LEU A  48 -1  N  SER A  47   O  CYS A 113
SHEET    6   A 6 ARG A  53  THR A  63 -1  O  LEU A  60   N  VAL A  42
CISPEP   1 SER A  103    PRO A  104          1        -0.01
CISPEP   2 SER A  103    PRO A  104          2         0.01
CISPEP   3 SER A  103    PRO A  104          3        -0.06
CISPEP   4 SER A  103    PRO A  104          4        -0.03
CISPEP   5 SER A  103    PRO A  104          5        -0.04
CISPEP   6 SER A  103    PRO A  104          6         0.00
CISPEP   7 SER A  103    PRO A  104          7        -0.12
CISPEP   8 SER A  103    PRO A  104          8        -0.04
CISPEP   9 SER A  103    PRO A  104          9        -0.10
CISPEP  10 SER A  103    PRO A  104         10         0.03
CISPEP  11 SER A  103    PRO A  104         11        -0.05
CISPEP  12 SER A  103    PRO A  104         12         0.04
CISPEP  13 SER A  103    PRO A  104         13        -0.03
CISPEP  14 SER A  103    PRO A  104         14        -0.06
CISPEP  15 SER A  103    PRO A  104         15        -0.04
CISPEP  16 SER A  103    PRO A  104         16        -0.06
CISPEP  17 SER A  103    PRO A  104         17        -0.01
CISPEP  18 SER A  103    PRO A  104         18         0.05
CISPEP  19 SER A  103    PRO A  104         19        -0.02
CISPEP  20 SER A  103    PRO A  104         20        -0.08
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
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      1.000000  0.000000  0.000000        0.00000
SCALE2      0.000000  1.000000  0.000000        0.00000
SCALE3      0.000000  0.000000  1.000000        0.00000
      
PROCHECK
Go to PROCHECK summary
 References