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PDBsum entry 2r17

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Top Page protein ligands Protein-protein interface(s) links
Protein transport PDB id
2r17
Jmol
Contents
Protein chains
183 a.a.
298 a.a.
276 a.a.
Ligands
GOL ×2
Waters ×49
HEADER    PROTEIN TRANSPORT                       22-AUG-07   2R17
TITLE     FUNCTIONAL ARCHITECTURE OF THE RETROMER CARGO-RECOGNITION COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29;
COMPND   3 CHAIN: A, B;
COMPND   4 SYNONYM: VESICLE PROTEIN SORTING 29, HVPS29, PEP11;
COMPND   5 ENGINEERED: YES;
COMPND   6 MOL_ID: 2;
COMPND   7 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35;
COMPND   8 CHAIN: C, D;
COMPND   9 SYNONYM: VESICLE PROTEIN SORTING 35, HVPS35, MATERNAL-EMBRYONIC 3;
COMPND  10 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: VPS29;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 MOL_ID: 2;
SOURCE  10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE  11 ORGANISM_COMMON: HUMAN;
SOURCE  12 ORGANISM_TAXID: 9606;
SOURCE  13 GENE: VPS35, MEM3;
SOURCE  14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE  15 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE  16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS    PROTEIN TRANSPORT, MEMBRANE, PHOSPHORYLATION
EXPDTA    X-RAY DIFFRACTION
AUTHOR    A.HIERRO,A.L.ROJAS,R.ROJAS,N.MURTHY,G.EFFANTIN,A.V.KAJAVA,A.C.STEVEN,
AUTHOR   2 J.S.BONIFACINO,J.H.HURLEY
REVDAT   3   13-JUL-11 2R17    1       VERSN
REVDAT   2   24-FEB-09 2R17    1       VERSN
REVDAT   1   30-OCT-07 2R17    0
JRNL        AUTH   A.HIERRO,A.L.ROJAS,R.ROJAS,N.MURTHY,G.EFFANTIN,A.V.KAJAVA,
JRNL        AUTH 2 A.C.STEVEN,J.S.BONIFACINO,J.H.HURLEY
JRNL        TITL   FUNCTIONAL ARCHITECTURE OF THE RETROMER CARGO-RECOGNITION
JRNL        TITL 2 COMPLEX.
JRNL        REF    NATURE                        V. 449  1063 2007
JRNL        REFN                   ISSN 0028-0836
JRNL        PMID   17891154
JRNL        DOI    10.1038/NATURE06216
REMARK   2
REMARK   2 RESOLUTION.    2.80 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS
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 : NULL
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 50.00
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)   (%) : 92.1
REMARK   3   NUMBER OF REFLECTIONS             : 27869
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) : 0.216
REMARK   3   FREE R VALUE                     : 0.268
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.600
REMARK   3   FREE R VALUE TEST SET COUNT      : 1390
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            : 7579
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 12
REMARK   3   SOLVENT ATOMS            : 49
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 54.73
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -23.69600
REMARK   3    B22 (A**2) : 12.03200
REMARK   3    B33 (A**2) : 11.66400
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  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) : 0.007
REMARK   3   BOND ANGLES            (DEGREES) : NULL
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) : 1.507 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 2.637 ; 2.000
REMARK   3   SIDE-CHAIN BOND              (A**2) : 2.210 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 3.376 ; 2.500
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : 25.75
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  : CNS_TOPPAR:PROTEIN_REP.PARAM
REMARK   3  PARAMETER FILE  2  : CNS_TOPPAR:WATER_REP.PARAM
REMARK   3  PARAMETER FILE  3  : GOL.PARAM
REMARK   3  PARAMETER FILE  4  : NULL
REMARK   3  PARAMETER FILE  5  : NULL
REMARK   3  PARAMETER FILE  6  : NULL
REMARK   3  TOPOLOGY FILE  1   : CNS_TOPPAR:PROTEIN.TOP
REMARK   3  TOPOLOGY FILE  2   : CNS_TOPPAR:DNA-RNA.TOP
REMARK   3  TOPOLOGY FILE  3   : CNS_TOPPAR:WATER.TOP
REMARK   3  TOPOLOGY FILE  4   : CNS_TOPPAR:ION.TOP
REMARK   3  TOPOLOGY FILE  5   : GOL.TOP
REMARK   3  TOPOLOGY FILE  6   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2R17 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-07.
REMARK 100 THE RCSB ID CODE IS RCSB044298.
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                             : 8.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : APS
REMARK 200  BEAMLINE                       : 22-ID
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.97926
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL
REMARK 200  DATA SCALING SOFTWARE          : HKL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 29916
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.800
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.8
REMARK 200  DATA REDUNDANCY                : 13.500
REMARK 200  R MERGE                    (I) : 0.09500
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 11.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.90
REMARK 200  COMPLETENESS FOR SHELL     (%) : 91.7
REMARK 200  DATA REDUNDANCY IN SHELL       : 9.80
REMARK 200  R MERGE FOR SHELL          (I) : 0.33200
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 54.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 1M NACL,50MM TRIS, PH
REMARK 280  8.0, HANGING DROP, TEMPERATURE 291K
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       33.12500
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       70.22600
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       64.23550
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       70.22600
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       33.12500
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       64.23550
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 300 REMARK: THE BIOLOGICAL UNIT IS A DIMER. THERE ARE 2 BIOLOGICAL
REMARK 300 UNITS IN THE ASYMMETRIC UNIT (CHAINS A & C AND CHAINS B & 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3250 ANGSTROM**2
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3480 ANGSTROM**2
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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     ASP D   483
REMARK 465     SER D   679
REMARK 465     GLY D   680
REMARK 465     ARG D   681
REMARK 465     ASN D   682
REMARK 465     THR D   683
REMARK 465     ASP D   684
REMARK 465     LYS D   685
REMARK 465     ASN D   686
REMARK 465     GLY D   687
REMARK 465     GLU D   688
REMARK 465     GLU D   689
REMARK 465     LEU D   690
REMARK 465     HIS D   691
REMARK 465     GLY D   692
REMARK 465     GLY D   693
REMARK 465     LYS D   694
REMARK 465     GLU D   734
REMARK 465     ASN D   735
REMARK 465     ASP D   736
REMARK 465     ALA D   737
REMARK 465     VAL D   738
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   O    LYS C   544     CB   SER C   547              2.13
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    ASP A   8       48.75     38.04
REMARK 500    THR A  37      -71.40    -77.91
REMARK 500    CYS A  41      -64.47     75.56
REMARK 500    ASP A  62        2.49    -65.87
REMARK 500    ASP A 107       48.67     70.49
REMARK 500    HIS A 115      -29.81     67.70
REMARK 500    ASN A 126       13.69     59.86
REMARK 500    PRO A 148      153.76    -47.87
REMARK 500    SER A 149      158.05    172.22
REMARK 500    GLN A 156      -65.98    -94.42
REMARK 500    ALA A 157      111.20   -172.12
REMARK 500    LYS A 181      147.95    -39.27
REMARK 500    ASN B  39       40.35     77.72
REMARK 500    CYS B  41      -53.38     87.25
REMARK 500    ASN B  66       98.66    -66.34
REMARK 500    HIS B 115      -35.35     74.96
REMARK 500    ALA B 135        3.29    -67.59
REMARK 500    SER B 149      149.42   -171.62
REMARK 500    GLN B 156      -71.59    -94.26
REMARK 500    ALA B 157      112.34   -179.60
REMARK 500    SER B 158       18.62     59.80
REMARK 500    ALA C 577      -64.12   -134.76
REMARK 500    ASN C 598        5.10     86.64
REMARK 500    GLU C 615      -73.50    -63.67
REMARK 500    ASP C 712      124.53   -170.52
REMARK 500    ASP C 736      -37.48    -35.02
REMARK 500    ASP D 551       33.54    -85.42
REMARK 500    ALA D 577      -56.55   -143.33
REMARK 500    LYS D 639       35.08   -140.28
REMARK 500    PHE D 677       42.58   -106.95
REMARK 500    ASN D 756       71.53   -106.20
REMARK 500    GLU D 758      141.30    -37.80
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    TRP A  93        24.4      L          L   OUTSIDE RANGE
REMARK 500    SER C 547        22.5      L          L   OUTSIDE RANGE
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 RESIDUE GOL D 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 2
DBREF  2R17 A    1   182  UNP    Q9UBQ0   VPS29_HUMAN      1    182
DBREF  2R17 B    1   182  UNP    Q9UBQ0   VPS29_HUMAN      1    182
DBREF  2R17 C  483   780  UNP    Q96QK1   VPS35_HUMAN    483    780
DBREF  2R17 D  483   780  UNP    Q96QK1   VPS35_HUMAN    483    780
SEQADV 2R17 MSE A    0  UNP  Q9UBQ0              INITIATING METHIONINE
SEQADV 2R17 MSE B    0  UNP  Q9UBQ0              INITIATING METHIONINE
SEQRES   1 A  183  MSE MSE LEU VAL LEU VAL LEU GLY ASP LEU HIS ILE PRO
SEQRES   2 A  183  HIS ARG CYS ASN SER LEU PRO ALA LYS PHE LYS LYS LEU
SEQRES   3 A  183  LEU VAL PRO GLY LYS ILE GLN HIS ILE LEU CYS THR GLY
SEQRES   4 A  183  ASN LEU CYS THR LYS GLU SER TYR ASP TYR LEU LYS THR
SEQRES   5 A  183  LEU ALA GLY ASP VAL HIS ILE VAL ARG GLY ASP PHE ASP
SEQRES   6 A  183  GLU ASN LEU ASN TYR PRO GLU GLN LYS VAL VAL THR VAL
SEQRES   7 A  183  GLY GLN PHE LYS ILE GLY LEU ILE HIS GLY HIS GLN VAL
SEQRES   8 A  183  ILE PRO TRP GLY ASP MSE ALA SER LEU ALA LEU LEU GLN
SEQRES   9 A  183  ARG GLN PHE ASP VAL ASP ILE LEU ILE SER GLY HIS THR
SEQRES  10 A  183  HIS LYS PHE GLU ALA PHE GLU HIS GLU ASN LYS PHE TYR
SEQRES  11 A  183  ILE ASN PRO GLY SER ALA THR GLY ALA TYR ASN ALA LEU
SEQRES  12 A  183  GLU THR ASN ILE ILE PRO SER PHE VAL LEU MSE ASP ILE
SEQRES  13 A  183  GLN ALA SER THR VAL VAL THR TYR VAL TYR GLN LEU ILE
SEQRES  14 A  183  GLY ASP ASP VAL LYS VAL GLU ARG ILE GLU TYR LYS LYS
SEQRES  15 A  183  PRO
SEQRES   1 B  183  MSE MSE LEU VAL LEU VAL LEU GLY ASP LEU HIS ILE PRO
SEQRES   2 B  183  HIS ARG CYS ASN SER LEU PRO ALA LYS PHE LYS LYS LEU
SEQRES   3 B  183  LEU VAL PRO GLY LYS ILE GLN HIS ILE LEU CYS THR GLY
SEQRES   4 B  183  ASN LEU CYS THR LYS GLU SER TYR ASP TYR LEU LYS THR
SEQRES   5 B  183  LEU ALA GLY ASP VAL HIS ILE VAL ARG GLY ASP PHE ASP
SEQRES   6 B  183  GLU ASN LEU ASN TYR PRO GLU GLN LYS VAL VAL THR VAL
SEQRES   7 B  183  GLY GLN PHE LYS ILE GLY LEU ILE HIS GLY HIS GLN VAL
SEQRES   8 B  183  ILE PRO TRP GLY ASP MSE ALA SER LEU ALA LEU LEU GLN
SEQRES   9 B  183  ARG GLN PHE ASP VAL ASP ILE LEU ILE SER GLY HIS THR
SEQRES  10 B  183  HIS LYS PHE GLU ALA PHE GLU HIS GLU ASN LYS PHE TYR
SEQRES  11 B  183  ILE ASN PRO GLY SER ALA THR GLY ALA TYR ASN ALA LEU
SEQRES  12 B  183  GLU THR ASN ILE ILE PRO SER PHE VAL LEU MSE ASP ILE
SEQRES  13 B  183  GLN ALA SER THR VAL VAL THR TYR VAL TYR GLN LEU ILE
SEQRES  14 B  183  GLY ASP ASP VAL LYS VAL GLU ARG ILE GLU TYR LYS LYS
SEQRES  15 B  183  PRO
SEQRES   1 C  298  ASP PHE ALA ASP GLU GLN SER LEU VAL GLY ARG PHE ILE
SEQRES   2 C  298  HIS LEU LEU ARG SER GLU ASP PRO ASP GLN GLN TYR LEU
SEQRES   3 C  298  ILE LEU ASN THR ALA ARG LYS HIS PHE GLY ALA GLY GLY
SEQRES   4 C  298  ASN GLN ARG ILE ARG PHE THR LEU PRO PRO LEU VAL PHE
SEQRES   5 C  298  ALA ALA TYR GLN LEU ALA PHE ARG TYR LYS GLU ASN SER
SEQRES   6 C  298  LYS VAL ASP ASP LYS TRP GLU LYS LYS CYS GLN LYS ILE
SEQRES   7 C  298  PHE SER PHE ALA HIS GLN THR ILE SER ALA LEU ILE LYS
SEQRES   8 C  298  ALA GLU LEU ALA GLU LEU PRO LEU ARG LEU PHE LEU GLN
SEQRES   9 C  298  GLY ALA LEU ALA ALA GLY GLU ILE GLY PHE GLU ASN HIS
SEQRES  10 C  298  GLU THR VAL ALA TYR GLU PHE MSE SER GLN ALA PHE SER
SEQRES  11 C  298  LEU TYR GLU ASP GLU ILE SER ASP SER LYS ALA GLN LEU
SEQRES  12 C  298  ALA ALA ILE THR LEU ILE ILE GLY THR PHE GLU ARG MSE
SEQRES  13 C  298  LYS CYS PHE SER GLU GLU ASN HIS GLU PRO LEU ARG THR
SEQRES  14 C  298  GLN CYS ALA LEU ALA ALA SER LYS LEU LEU LYS LYS PRO
SEQRES  15 C  298  ASP GLN GLY ARG ALA VAL SER THR CYS ALA HIS LEU PHE
SEQRES  16 C  298  TRP SER GLY ARG ASN THR ASP LYS ASN GLY GLU GLU LEU
SEQRES  17 C  298  HIS GLY GLY LYS ARG VAL MSE GLU CYS LEU LYS LYS ALA
SEQRES  18 C  298  LEU LYS ILE ALA ASN GLN CYS MSE ASP PRO SER LEU GLN
SEQRES  19 C  298  VAL GLN LEU PHE ILE GLU ILE LEU ASN ARG TYR ILE TYR
SEQRES  20 C  298  PHE TYR GLU LYS GLU ASN ASP ALA VAL THR ILE GLN VAL
SEQRES  21 C  298  LEU ASN GLN LEU ILE GLN LYS ILE ARG GLU ASP LEU PRO
SEQRES  22 C  298  ASN LEU GLU SER SER GLU GLU THR GLU GLN ILE ASN LYS
SEQRES  23 C  298  HIS PHE HIS ASN THR LEU GLU HIS LEU ARG LEU ARG
SEQRES   1 D  298  ASP PHE ALA ASP GLU GLN SER LEU VAL GLY ARG PHE ILE
SEQRES   2 D  298  HIS LEU LEU ARG SER GLU ASP PRO ASP GLN GLN TYR LEU
SEQRES   3 D  298  ILE LEU ASN THR ALA ARG LYS HIS PHE GLY ALA GLY GLY
SEQRES   4 D  298  ASN GLN ARG ILE ARG PHE THR LEU PRO PRO LEU VAL PHE
SEQRES   5 D  298  ALA ALA TYR GLN LEU ALA PHE ARG TYR LYS GLU ASN SER
SEQRES   6 D  298  LYS VAL ASP ASP LYS TRP GLU LYS LYS CYS GLN LYS ILE
SEQRES   7 D  298  PHE SER PHE ALA HIS GLN THR ILE SER ALA LEU ILE LYS
SEQRES   8 D  298  ALA GLU LEU ALA GLU LEU PRO LEU ARG LEU PHE LEU GLN
SEQRES   9 D  298  GLY ALA LEU ALA ALA GLY GLU ILE GLY PHE GLU ASN HIS
SEQRES  10 D  298  GLU THR VAL ALA TYR GLU PHE MSE SER GLN ALA PHE SER
SEQRES  11 D  298  LEU TYR GLU ASP GLU ILE SER ASP SER LYS ALA GLN LEU
SEQRES  12 D  298  ALA ALA ILE THR LEU ILE ILE GLY THR PHE GLU ARG MSE
SEQRES  13 D  298  LYS CYS PHE SER GLU GLU ASN HIS GLU PRO LEU ARG THR
SEQRES  14 D  298  GLN CYS ALA LEU ALA ALA SER LYS LEU LEU LYS LYS PRO
SEQRES  15 D  298  ASP GLN GLY ARG ALA VAL SER THR CYS ALA HIS LEU PHE
SEQRES  16 D  298  TRP SER GLY ARG ASN THR ASP LYS ASN GLY GLU GLU LEU
SEQRES  17 D  298  HIS GLY GLY LYS ARG VAL MSE GLU CYS LEU LYS LYS ALA
SEQRES  18 D  298  LEU LYS ILE ALA ASN GLN CYS MSE ASP PRO SER LEU GLN
SEQRES  19 D  298  VAL GLN LEU PHE ILE GLU ILE LEU ASN ARG TYR ILE TYR
SEQRES  20 D  298  PHE TYR GLU LYS GLU ASN ASP ALA VAL THR ILE GLN VAL
SEQRES  21 D  298  LEU ASN GLN LEU ILE GLN LYS ILE ARG GLU ASP LEU PRO
SEQRES  22 D  298  ASN LEU GLU SER SER GLU GLU THR GLU GLN ILE ASN LYS
SEQRES  23 D  298  HIS PHE HIS ASN THR LEU GLU HIS LEU ARG LEU ARG
MODRES 2R17 MSE A    0  MET  SELENOMETHIONINE
MODRES 2R17 MSE A    1  MET  SELENOMETHIONINE
MODRES 2R17 MSE A   96  MET  SELENOMETHIONINE
MODRES 2R17 MSE A  153  MET  SELENOMETHIONINE
MODRES 2R17 MSE B    0  MET  SELENOMETHIONINE
MODRES 2R17 MSE B    1  MET  SELENOMETHIONINE
MODRES 2R17 MSE B   96  MET  SELENOMETHIONINE
MODRES 2R17 MSE B  153  MET  SELENOMETHIONINE
MODRES 2R17 MSE C  607  MET  SELENOMETHIONINE
MODRES 2R17 MSE C  638  MET  SELENOMETHIONINE
MODRES 2R17 MSE C  697  MET  SELENOMETHIONINE
MODRES 2R17 MSE C  711  MET  SELENOMETHIONINE
MODRES 2R17 MSE D  607  MET  SELENOMETHIONINE
MODRES 2R17 MSE D  638  MET  SELENOMETHIONINE
MODRES 2R17 MSE D  697  MET  SELENOMETHIONINE
MODRES 2R17 MSE D  711  MET  SELENOMETHIONINE
HET    MSE  A   0       8
HET    MSE  A   1       8
HET    MSE  A  96       8
HET    MSE  A 153       8
HET    MSE  B   0       8
HET    MSE  B   1       8
HET    MSE  B  96       8
HET    MSE  B 153       8
HET    MSE  C 607       8
HET    MSE  C 638       8
HET    MSE  C 697       8
HET    MSE  C 711       8
HET    MSE  D 607       8
HET    MSE  D 638       8
HET    MSE  D 697       8
HET    MSE  D 711       8
HET    GOL  D   1       6
HET    GOL  D   2       6
HETNAM     MSE SELENOMETHIONINE
HETNAM     GOL GLYCEROL
HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL   1  MSE    16(C5 H11 N O2 SE)
FORMUL   5  GOL    2(C3 H8 O3)
FORMUL   7  HOH   *49(H2 O)
HELIX    1   1 PRO A   19  LEU A   26  1                                   8
HELIX    2   2 THR A   42  ALA A   53  1                                  12
HELIX    3   3 ASP A   95  ASP A  107  1                                  13
HELIX    4   4 PRO B   19  LEU B   26  1                                   8
HELIX    5   5 THR B   42  ALA B   53  1                                  12
HELIX    6   6 ASP B   95  ASP B  107  1                                  13
HELIX    7   7 GLU C  487  ARG C  499  1                                  13
HELIX    8   8 ASP C  502  ALA C  519  1                                  18
HELIX    9   9 ARG C  524  GLU C  545  1                                  22
HELIX   10  10 LYS C  552  ALA C  574  1                                  23
HELIX   11  11 ALA C  577  GLY C  595  1                                  19
HELIX   12  12 ASN C  598  ILE C  618  1                                  21
HELIX   13  13 ASP C  620  GLU C  636  1                                  17
HELIX   14  14 SER C  642  LYS C  659  1                                  18
HELIX   15  15 LYS C  662  CYS C  673  1                                  12
HELIX   16  16 CYS C  673  SER C  679  1                                   7
HELIX   17  17 GLY C  692  CYS C  710  1                                  19
HELIX   18  18 ASP C  712  GLU C  732  1                                  21
HELIX   19  19 THR C  739  GLU C  752  1                                  14
HELIX   20  20 SER C  760  LEU C  777  1                                  18
HELIX   21  21 PHE D  484  LEU D  498  1                                  15
HELIX   22  22 ASP D  502  GLY D  518  1                                  17
HELIX   23  23 ARG D  524  LEU D  529  1                                   6
HELIX   24  24 LEU D  529  ASN D  546  1                                  18
HELIX   25  25 SER D  547  VAL D  549  5                                   3
HELIX   26  26 LYS D  552  ALA D  574  1                                  23
HELIX   27  27 ALA D  577  GLY D  595  1                                  19
HELIX   28  28 ASN D  598  ILE D  618  1                                  21
HELIX   29  29 ASP D  620  MSE D  638  1                                  19
HELIX   30  30 SER D  642  LEU D  660  1                                  19
HELIX   31  31 LYS D  662  ALA D  674  1                                  13
HELIX   32  32 HIS D  675  TRP D  678  5                                   4
HELIX   33  33 ARG D  695  GLN D  709  1                                  15
HELIX   34  34 ASP D  712  GLU D  732  1                                  21
HELIX   35  35 GLN D  741  LEU D  754  1                                  14
HELIX   36  36 SER D  760  LEU D  777  1                                  18
SHEET    1   A 6 VAL A  56  ILE A  58  0
SHEET    2   A 6 HIS A  33  CYS A  36  1  N  CYS A  36   O  HIS A  57
SHEET    3   A 6 MSE A   1  LEU A   6  1  N  LEU A   4   O  LEU A  35
SHEET    4   A 6 SER A 149  ILE A 155 -1  O  ILE A 155   N  MSE A   1
SHEET    5   A 6 VAL A 160  GLN A 166 -1  O  TYR A 165   N  PHE A 150
SHEET    6   A 6 LYS A 173  TYR A 179 -1  O  TYR A 179   N  VAL A 160
SHEET    1   B 5 GLN A  72  VAL A  77  0
SHEET    2   B 5 PHE A  80  ILE A  85 -1  O  PHE A  80   N  VAL A  77
SHEET    3   B 5 ILE A 110  ILE A 112  1  O  ILE A 110   N  GLY A  83
SHEET    4   B 5 LYS A 127  ASN A 131  1  O  PHE A 128   N  LEU A 111
SHEET    5   B 5 GLU A 120  HIS A 124 -1  N  PHE A 122   O  TYR A 129
SHEET    1   C 6 ASP B  55  ILE B  58  0
SHEET    2   C 6 HIS B  33  CYS B  36  1  N  CYS B  36   O  HIS B  57
SHEET    3   C 6 MSE B   1  LEU B   6  1  N  LEU B   4   O  HIS B  33
SHEET    4   C 6 SER B 149  ILE B 155 -1  O  VAL B 151   N  VAL B   5
SHEET    5   C 6 THR B 159  ILE B 168 -1  O  TYR B 165   N  PHE B 150
SHEET    6   C 6 ASP B 171  LYS B 180 -1  O  ILE B 177   N  THR B 162
SHEET    1   D 5 GLN B  72  VAL B  77  0
SHEET    2   D 5 PHE B  80  ILE B  85 -1  O  LEU B  84   N  LYS B  73
SHEET    3   D 5 ILE B 110  ILE B 112  1  O  ILE B 112   N  GLY B  83
SHEET    4   D 5 LYS B 127  ASN B 131  1  O  PHE B 128   N  LEU B 111
SHEET    5   D 5 GLU B 120  HIS B 124 -1  N  GLU B 120   O  ASN B 131
LINK         C   MSE A   0                 N   MSE A   1     1555   1555  1.33
LINK         C   MSE A   1                 N   LEU A   2     1555   1555  1.34
LINK         C   ASP A  95                 N   MSE A  96     1555   1555  1.33
LINK         C   MSE A  96                 N   ALA A  97     1555   1555  1.33
LINK         C   LEU A 152                 N   MSE A 153     1555   1555  1.33
LINK         C   MSE A 153                 N   ASP A 154     1555   1555  1.33
LINK         C   MSE B   0                 N   MSE B   1     1555   1555  1.33
LINK         C   MSE B   1                 N   LEU B   2     1555   1555  1.34
LINK         C   ASP B  95                 N   MSE B  96     1555   1555  1.33
LINK         C   MSE B  96                 N   ALA B  97     1555   1555  1.33
LINK         C   LEU B 152                 N   MSE B 153     1555   1555  1.33
LINK         C   MSE B 153                 N   ASP B 154     1555   1555  1.34
LINK         C   PHE C 606                 N   MSE C 607     1555   1555  1.33
LINK         C   MSE C 607                 N   SER C 608     1555   1555  1.33
LINK         C   ARG C 637                 N   MSE C 638     1555   1555  1.33
LINK         C   MSE C 638                 N   LYS C 639     1555   1555  1.33
LINK         C   VAL C 696                 N   MSE C 697     1555   1555  1.33
LINK         C   MSE C 697                 N   GLU C 698     1555   1555  1.33
LINK         C   CYS C 710                 N   MSE C 711     1555   1555  1.33
LINK         C   MSE C 711                 N   ASP C 712     1555   1555  1.32
LINK         C   PHE D 606                 N   MSE D 607     1555   1555  1.34
LINK         C   MSE D 607                 N   SER D 608     1555   1555  1.32
LINK         C   ARG D 637                 N   MSE D 638     1555   1555  1.32
LINK         C   MSE D 638                 N   LYS D 639     1555   1555  1.33
LINK         C   VAL D 696                 N   MSE D 697     1555   1555  1.33
LINK         C   MSE D 697                 N   GLU D 698     1555   1555  1.33
LINK         C   CYS D 710                 N   MSE D 711     1555   1555  1.33
LINK         C   MSE D 711                 N   ASP D 712     1555   1555  1.33
CISPEP   1 ILE A   11    PRO A   12          0         0.02
CISPEP   2 ILE A   91    PRO A   92          0         0.20
CISPEP   3 ILE B   11    PRO B   12          0         0.18
CISPEP   4 ILE B   91    PRO B   92          0        -0.11
SITE     1 AC1  3 ALA D 577  GLU D 578  LEU D 579
SITE     1 AC2  2 HOH C 787  ASN D 744
CRYST1   66.250  128.471  140.452  90.00  90.00  90.00 P 21 21 21    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      0.015094  0.000000  0.000000        0.00000
SCALE2      0.000000  0.007784  0.000000        0.00000
SCALE3      0.000000  0.000000  0.007120        0.00000
      
PROCHECK
Go to PROCHECK summary
 References