Header list of 2bgf.pdb file
Complete list - r 25 2 Bytes
HEADER UBIQUITIN 22-DEC-04 2BGF
TITLE NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL
TITLE 2 SHIFT PERTURBATION DATA TOGETHER WITH RDCS AND 15N-
TITLE 3 RELAXATION DATA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DI-UBIQUITIN;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: UBIQUITIN;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: ISOPEPTIDE BOND BETWEEN GLY76A AND LYS48B
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;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PROTEASOME, DEGRADATION, UBIQUITIN, POLYUBIQUITIN
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.D.J.VAN DIJK,D.FUSHMAN,A.M.J.J.BONVIN
REVDAT 2 24-FEB-09 2BGF 1 VERSN
REVDAT 1 31-AUG-05 2BGF 0
JRNL AUTH A.D.J.VAN DIJK,D.FUSHMAN,A.M.J.J.BONVIN
JRNL TITL VARIOUS STRATEGIES OF USING RESIDUAL DIPOLAR
JRNL TITL 2 COUPLINGS IN NMR-DRIVEN PROTEIN DOCKING:
JRNL TITL 3 APPLICATION TO LYS48-LINKED DI-UBIQUITIN AND
JRNL TITL 4 VALIDATION AGAINST 15N-RELAXATION DATA
JRNL REF PROTEINS: STRUCT., FUNCT., V. 60 367 2005
JRNL REF 2 BIOINF.
JRNL REFN ISSN 0887-3585
JRNL PMID 15937902
JRNL DOI 10.1002/PROT.20476
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH R.VARADAN,O.WALKER,C.PICKART,D.FUSHMAN
REMARK 1 TITL STRUCTURAL PROPERTIES OF POLYUBIQUITIN CHAINS IN
REMARK 1 TITL 2 SOLUTION
REMARK 1 REF J.MOL.BIOL. V. 324 637 2002
REMARK 1 REFN ISSN 0022-2836
REMARK 1 PMID 12460567
REMARK 1 DOI 10.1016/S0022-2836(02)01198-1
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : HADDOCK
REMARK 3 AUTHORS : DOMINGUEZ, BOELENS,BONVIN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IS DONE IN EXPLICIT
REMARK 3 SOLVENT. REFINEMENT AND STRUCTURE CALCULATION DETAILS CAN BE
REMARK 3 FOUND IN DOMINGUEZ ET AL, JACS 2003, 125, 173
REMARK 4
REMARK 4 2BGF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-04.
REMARK 100 THE PDBE ID CODE IS EBI-22088.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298.0
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 20MM
REMARK 210 PRESSURE : 1.0
REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D20
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC, TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600
REMARK 210 SPECTROMETER MODEL : OTHER
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : HADDOCK
REMARK 210 METHOD USED : HADDOCK
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES
REMARK 210 OF LOWEST ENERGY CLUSTER
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING
REMARK 210 CHEMICAL SHIFT PERTURBATION DATA AS AMBIGUOUS INTERACTION
REMARK 210 RESTRAINTS AND RESIDUAL DIPOLAR COUPLINGS BOTH AS DIRECT
REMARK 210 RESTRAINTS (SANI) AND INTERVECTOR PROJECTION ANGLE
REMARK 210 RESTRAINTS (VEAN).
REMARK 210
REMARK 210 STRUCTURAL CHARACTERISTICS OF ENSEMBLE OF 10 BEST:
REMARK 210 AVERAGE (STANDARD DEVIATION)
REMARK 210 INTERMOLECULAR ENERGIES
REMARK 210 EVDW (KCAL/MOL) : -61 (9)
REMARK 210 EELEC (KCAL/MOL) : -425 (35)
REMARK 210
REMARK 210 BACKBONE RMSD (A) : 0.7 (0.2)
REMARK 210
REMARK 210 BURIED SURFACE AREA (A2) : 1749 (54)
REMARK 210
REMARK 210 RAMACHANDRAN ANALYSIS:
REMARK 210 MOST FAVORED (%) : 87.0
REMARK 210 ADDITIONAL ALLOWED(%) : 13.0
REMARK 210 GENEROUSLY ALLOWED (%) : 0.0
REMARK 210 DISALLOWED (%) : 0.0
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 400
REMARK 400 COMPOUND
REMARK 400 FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF
REMARK 400 CELLULAR PROTEINS, MAINTENANCE OF CHROMATIN STRUCTURE,
REMARK 400 REGULATION OF GENE EXPRESSION, STRESS RESPONSE, AND
REMARK 400 RIBOSOME BIOGENESIS
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 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 GLU A 16 79.95 -105.17
REMARK 500 1 LYS A 33 -83.42 -80.90
REMARK 500 1 GLN A 62 -167.04 -119.23
REMARK 500 1 GLU A 64 12.26 59.83
REMARK 500 1 LYS B 11 140.38 -175.53
REMARK 500 1 LYS B 33 -76.46 -100.94
REMARK 500 2 LYS A 33 -80.51 -81.79
REMARK 500 2 LYS B 33 -69.20 -108.80
REMARK 500 3 GLU A 16 77.00 -112.36
REMARK 500 3 LYS A 33 -83.72 -84.78
REMARK 500 3 LEU A 67 -164.70 -113.92
REMARK 500 3 LYS B 33 -76.21 -107.33
REMARK 500 4 GLU A 16 77.83 -105.40
REMARK 500 4 LYS A 33 -79.17 -80.93
REMARK 500 4 GLN A 62 -163.91 -123.43
REMARK 500 4 GLU A 64 14.44 56.51
REMARK 500 4 GLN B 62 -161.45 -110.16
REMARK 500 5 LYS A 33 -80.98 -84.09
REMARK 500 5 GLN A 62 -159.47 -127.23
REMARK 500 5 LYS B 33 -73.54 -111.25
REMARK 500 5 LEU B 73 -109.12 -80.53
REMARK 500 6 GLU A 16 78.62 -114.41
REMARK 500 6 LYS A 33 -83.37 -76.60
REMARK 500 6 GLN A 62 -165.24 -128.22
REMARK 500 6 ARG A 72 57.64 -90.39
REMARK 500 6 LYS B 33 -66.94 -108.94
REMARK 500 6 GLN B 62 -165.57 -103.43
REMARK 500 7 GLU A 16 76.47 -103.55
REMARK 500 7 LYS A 33 -84.80 -79.60
REMARK 500 7 GLU A 64 10.15 58.33
REMARK 500 7 ARG A 72 64.67 -112.26
REMARK 500 7 LYS B 33 -76.92 -108.60
REMARK 500 7 GLN B 62 -167.84 -105.01
REMARK 500 8 LYS A 33 -83.02 -81.68
REMARK 500 8 LYS B 33 -68.22 -108.96
REMARK 500 8 ASN B 60 32.62 71.71
REMARK 500 9 LYS A 33 -77.61 -85.35
REMARK 500 9 GLN A 62 -159.10 -136.98
REMARK 500 9 LEU A 73 -164.66 -105.75
REMARK 500 9 GLN B 62 -164.76 -105.08
REMARK 500 10 LYS A 33 -78.54 -90.03
REMARK 500 10 GLN A 62 -166.14 -118.18
REMARK 500 10 GLU A 64 13.04 58.95
REMARK 500 10 LEU A 73 -83.15 -82.14
REMARK 500 10 LYS B 33 -72.92 -102.79
REMARK 500 10 ASN B 60 45.14 70.50
REMARK 500 10 GLN B 62 -168.10 -115.69
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AAR RELATED DB: PDB
REMARK 900 DI-UBIQUITIN
REMARK 900 RELATED ID: 1E0Q RELATED DB: PDB
REMARK 900 MUTANT PEPTIDE FROM THE FIRST N-TERMINAL
REMARK 900 17 AMINO-ACID OF UBIQUITIN
REMARK 900 RELATED ID: 1P3Q RELATED DB: PDB
REMARK 900 MECHANISM OF UBIQUITIN RECOGNITION BY THE
REMARK 900 CUE DOMAIN OF VPS9
REMARK 900 RELATED ID: 1UZX RELATED DB: PDB
REMARK 900 A COMPLEX OF THE VPS23 UEV WITH UBIQUITIN
DBREF 2BGF A 1 76 UNP P62988 UBIQ_HUMAN 1 76
DBREF 2BGF B 1 76 UNP P62988 UBIQ_HUMAN 1 76
SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE
SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL
SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP
SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP
SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER
SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY
HELIX 1 1 THR A 22 GLU A 34 1 13
HELIX 2 2 PRO A 37 ASP A 39 5 3
HELIX 3 3 LEU A 56 ASN A 60 5 5
HELIX 4 4 THR B 22 GLU B 34 1 13
HELIX 5 5 PRO B 37 ASP B 39 5 3
HELIX 6 6 LEU B 56 ASN B 60 5 5
SHEET 1 AA 5 LYS A 11 GLU A 16 0
SHEET 2 AA 5 GLN A 2 THR A 7 -1 O ILE A 3 N LEU A 15
SHEET 3 AA 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6
SHEET 4 AA 5 GLN A 41 PHE A 45 -1 O ARG A 42 N VAL A 70
SHEET 5 AA 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45
SHEET 1 BA 5 THR B 12 GLU B 16 0
SHEET 2 BA 5 GLN B 2 THR B 7 -1 O ILE B 3 N LEU B 15
SHEET 3 BA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6
SHEET 4 BA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70
SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45
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
MODEL 1
Complete list - r 25 2 Bytes