Header list of 1ur6.pdb file
Complete list - r 25 2 Bytes
HEADER LIGASE 27-OCT-03 1UR6
TITLE NMR BASED STRUCTURAL MODEL OF THE UBCH5B-CNOT4 COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: UBCH5B, UBIQUITIN CARRIER PROTEIN, E2(17)KB 2;
COMPND 5 EC: 6.3.2.19;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP;
COMPND 8 CHAIN: B;
COMPND 9 FRAGMENT: RING FINGER, RESIDUES 12-63;
COMPND 10 SYNONYM: CNOT4, NOT4H
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 7 ORGANISM_COMMON: HUMAN;
SOURCE 8 ORGANISM_TAXID: 9606
KEYWDS LIGASE, UBIQUITIN CONJUGATING ENZYME, UBIQUITIN LIGASE,
KEYWDS 2 RING FINGER PROTEIN, CCR4-NOT COMPLEX, TRANSCRIPTION
KEYWDS 3 REGULATION
EXPDTA SOLUTION NMR; THEORETICAL MODEL
NUMMDL 5
AUTHOR C.DOMINGUEZ,A.M.J.J.BONVIN,G.S.WINKLER,F.M.A.VAN SCHAIK,
AUTHOR 2 H.TH.M.TIMMERS,R.BOELENS
REVDAT 2 24-FEB-09 1UR6 1 VERSN
REVDAT 1 07-MAY-04 1UR6 0
JRNL AUTH C.DOMINGUEZ,A.M.J.J.BONVIN,G.S.WINKLER,
JRNL AUTH 2 F.M.A.VAN SCHAIK,H.TH.M.TIMMERS,R.BOELENS
JRNL TITL STRUCTURAL MODEL OF THE UBCH5B/CNOT4 COMPLEX
JRNL TITL 2 REVEALED BY COMBINING NMR, MUTAGENESIS, AND
JRNL TITL 3 DOCKING APPROACHES
JRNL REF STRUCTURE V. 12 633 2004
JRNL REFN ISSN 0969-2126
JRNL PMID 15062086
JRNL DOI 10.1016/J.STR.2004.03.004
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
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,READ,
REMARK 3 RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS AS DESCIRIBED IN
REMARK 3 C. DOMINGUEZ ET AL. (2003), J.AM.CHEM.SOC, 125, P1731
REMARK 4
REMARK 4 1UR6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-03.
REMARK 100 THE PDBE ID CODE IS EBI-13704.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : NULL
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NONE
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 220
REMARK 220 EXPERIMENTAL DETAILS
REMARK 220 EXPERIMENT TYPE: THEORETICAL MODELLING
REMARK 220 MODELLING PROGRAM: HADDOCK1.1
REMARK 220 PROGRAM AUTHORS: C. DOMINGUEZ, R. BOELENS, A.M.J.J. BONVIN
REMARK 220 MODELLING EXPERIMENT: UBCH5B IS A HOMOLOGY MODEL BASED ON
REMARK 220 THE STRUCTURE OF THE YEAST UBC4. CNOT4 CORRESPOND TO THE
REMARK 220 NMR STRUCTURES (PDB:1E4U). THE CONSTRAINTS TO DRIVE THE
REMARK 220 DOCKING ARE DERIVED FROM NMR TITRATION EXPERIMENTS AND
REMARK 220 MUTAGENESIS DATA
REMARK 225
REMARK 225 THEORETICAL MODEL
REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE.
REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND
REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE
REMARK 225 RECORDS ARE MEANINGLESS.
REMARK 400
REMARK 400 COMPOUND
REMARK 400 CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS
REMARK 400 ATP + UBIQUITIN + PROTEIN LYSINE = AMP + DIPHOSPHATE + PROTEIN
REMARK 400 N-UBIQUITYLLYSINE.
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 H3 MET A 1 - OE2 GLU B 19 1.59
REMARK 500 HD11 LEU A 3 - HD11 ILE A 6 1.50
REMARK 500 HD2 PRO A 40 - HB2 TYR A 45 1.46
REMARK 500 HZ2 LYS A 63 - OD2 ASP B 48 1.56
REMARK 500 HE1 HIS A 75 - HG LEU A 109 1.58
REMARK 500 HB2 ASN A 79 - HB2 SER A 83 1.55
REMARK 500 OE2 GLU A 140 - HZ2 LYS A 144 1.59
REMARK 500 HB3 CYS B 14 - HD23 LEU B 21 1.52
REMARK 500 HB2 CYS B 31 - HE1 TYR B 60 1.43
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 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 PRO A 18 -157.27 -70.01
REMARK 500 1 GLN A 20 -48.54 74.95
REMARK 500 1 GLN A 34 65.53 -108.98
REMARK 500 1 VAL A 49 88.82 -162.58
REMARK 500 1 PRO A 61 32.51 -83.36
REMARK 500 1 PHE A 62 -33.81 -148.73
REMARK 500 1 GLN A 92 -164.11 66.55
REMARK 500 1 TRP A 93 -176.23 -171.66
REMARK 500 1 PRO A 95 -84.82 -15.03
REMARK 500 1 ASP A 112 93.56 61.74
REMARK 500 1 PRO A 113 178.75 -59.02
REMARK 500 1 PRO A 118 -115.73 -95.66
REMARK 500 1 PHE B 40 33.23 -77.15
REMARK 500 1 CYS B 41 -47.67 -145.32
REMARK 500 1 ALA B 55 24.86 -140.45
REMARK 500 1 CYS B 56 -28.08 -148.18
REMARK 500 1 ARG B 57 -1.38 72.47
REMARK 500 2 ALA A 2 57.57 -152.20
REMARK 500 2 ALA A 19 112.46 -171.94
REMARK 500 2 GLN A 20 -28.76 73.32
REMARK 500 2 PRO A 44 39.26 -75.55
REMARK 500 2 VAL A 49 85.07 -163.17
REMARK 500 2 PRO A 57 -154.34 -80.08
REMARK 500 2 PHE A 62 -37.39 -140.44
REMARK 500 2 SER A 91 62.99 63.47
REMARK 500 2 GLN A 92 101.17 67.05
REMARK 500 2 ASP A 112 88.49 64.15
REMARK 500 2 PRO A 113 172.93 -58.32
REMARK 500 2 PRO A 118 -135.24 -87.02
REMARK 500 2 PRO B 15 -67.09 -22.31
REMARK 500 2 ILE B 37 -157.34 -129.49
REMARK 500 2 PHE B 40 35.47 -87.36
REMARK 500 2 CYS B 41 -50.75 -149.61
REMARK 500 2 CYS B 56 -21.09 139.45
REMARK 500 3 VAL A 49 57.32 -150.38
REMARK 500 3 PRO A 57 -158.81 -75.02
REMARK 500 3 PRO A 61 36.56 -83.20
REMARK 500 3 PHE A 62 -54.61 -146.60
REMARK 500 3 GLN A 92 110.64 69.46
REMARK 500 3 LEU A 97 -151.02 -140.15
REMARK 500 3 ASP A 112 79.62 60.36
REMARK 500 3 PRO A 113 177.02 -59.40
REMARK 500 3 PRO A 118 -118.96 -86.87
REMARK 500 3 CYS B 17 -24.37 -156.26
REMARK 500 3 MET B 18 31.40 75.15
REMARK 500 3 TYR B 35 112.06 -160.24
REMARK 500 3 ARG B 46 42.14 -90.90
REMARK 500 3 THR B 47 -53.81 -156.13
REMARK 500 3 GLU B 49 -165.99 -79.30
REMARK 500 3 CYS B 56 -5.52 95.42
REMARK 500 3 ARG B 57 73.92 40.38
REMARK 500 3 PRO B 61 109.75 -55.58
REMARK 500 4 ASP A 28 -26.54 -179.38
REMARK 500 4 PRO A 57 -142.93 -74.38
REMARK 500 4 TYR A 60 -52.13 -139.63
REMARK 500 4 PHE A 62 -53.97 -130.52
REMARK 500 4 PRO A 65 -177.76 -68.03
REMARK 500 4 GLN A 92 114.87 66.64
REMARK 500 4 ALA A 96 33.68 -82.92
REMARK 500 4 ASP A 112 92.88 62.06
REMARK 500 4 PRO A 113 -167.74 -71.42
REMARK 500 4 PRO A 118 -125.93 -84.94
REMARK 500 4 LEU B 21 -164.04 -121.99
REMARK 500 4 ARG B 44 -54.48 -123.16
REMARK 500 4 ARG B 46 33.51 -90.57
REMARK 500 4 THR B 47 -57.20 -142.41
REMARK 500 4 CYS B 56 -25.89 -154.43
REMARK 500 4 ARG B 57 -11.34 76.13
REMARK 500 5 ILE A 6 22.91 -79.33
REMARK 500 5 HIS A 7 -55.33 -134.99
REMARK 500 5 PRO A 18 -170.75 -67.17
REMARK 500 5 GLN A 20 -47.78 73.96
REMARK 500 5 VAL A 49 84.94 -152.25
REMARK 500 5 PRO A 61 26.60 -77.44
REMARK 500 5 PHE A 62 -56.44 -139.85
REMARK 500 5 GLN A 92 110.72 64.43
REMARK 500 5 PRO A 95 -77.56 -34.44
REMARK 500 5 ALA A 96 57.73 -95.00
REMARK 500 5 ASP A 112 88.49 67.37
REMARK 500 5 PRO A 118 -130.29 -87.83
REMARK 500 5 CYS B 17 30.97 -161.09
REMARK 500 5 MET B 18 84.07 30.81
REMARK 500 5 THR B 47 -50.76 -135.36
REMARK 500 5 PRO B 54 -98.50 -54.64
REMARK 500 5 CYS B 56 -32.27 -155.11
REMARK 500 5 PRO B 59 -175.93 -66.64
REMARK 500 5 PRO B 61 -166.27 -73.34
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 79 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 41 SG
REMARK 620 2 CYS B 17 SG 79.7
REMARK 620 3 CYS B 14 SG 84.5 81.2
REMARK 620 4 CYS B 38 SG 79.9 156.9 86.2
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 80 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 31 SG
REMARK 620 2 CYS B 33 SG 79.9
REMARK 620 3 CYS B 56 SG 170.2 98.2
REMARK 620 4 CYS B 53 SG 88.9 85.8 81.3
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 79
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 80
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1E4U RELATED DB: PDB
REMARK 900 N-TERMINAL RING FINGER DOMAIN OF HUMAN NOT-4
DBREF 1UR6 A 1 147 UNP P51669 UB5B_HUMAN 1 147
DBREF 1UR6 B 12 63 UNP O95628 O95628 12 63
SEQRES 1 A 147 MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU
SEQRES 2 A 147 ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO VAL
SEQRES 3 A 147 GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY
SEQRES 4 A 147 PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU
SEQRES 5 A 147 THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO
SEQRES 6 A 147 LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE
SEQRES 7 A 147 ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG SER
SEQRES 8 A 147 GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU
SEQRES 9 A 147 SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP
SEQRES 10 A 147 PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP
SEQRES 11 A 147 ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN
SEQRES 12 A 147 LYS TYR ALA MET
SEQRES 1 B 52 VAL GLU CYS PRO LEU CYS MET GLU PRO LEU GLU ILE ASP
SEQRES 2 B 52 ASP ILE ASN PHE PHE PRO CYS THR CYS GLY TYR GLN ILE
SEQRES 3 B 52 CYS ARG PHE CYS TRP HIS ARG ILE ARG THR ASP GLU ASN
SEQRES 4 B 52 GLY LEU CYS PRO ALA CYS ARG LYS PRO TYR PRO GLU ASP
HET ZN B 79 1
HET ZN B 80 1
HETNAM ZN ZINC ION
FORMUL 3 ZN 2(ZN 2+)
HELIX 1 1 LEU A 3 ASP A 16 1 14
HELIX 2 2 LEU A 86 ARG A 90 5 5
HELIX 3 3 THR A 98 CYS A 111 1 14
HELIX 4 4 PRO A 121 ASP A 130 1 10
HELIX 5 5 ASP A 130 TYR A 145 1 16
HELIX 6 6 GLU B 22 ILE B 26 5 5
HELIX 7 7 CYS B 38 ARG B 46 1 9
SHEET 1 AA 3 HIS A 32 ILE A 37 0
SHEET 2 AA 3 PHE A 50 HIS A 55 -1 O PHE A 50 N ILE A 37
SHEET 3 AA 3 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55
LINK ZN ZN B 79 SG CYS B 41 1555 1555 2.45
LINK ZN ZN B 79 SG CYS B 17 1555 1555 2.46
LINK ZN ZN B 79 SG CYS B 14 1555 1555 2.47
LINK ZN ZN B 79 SG CYS B 38 1555 1555 2.35
LINK ZN ZN B 80 SG CYS B 33 1555 1555 2.51
LINK ZN ZN B 80 SG CYS B 56 1555 1555 2.41
LINK ZN ZN B 80 SG CYS B 53 1555 1555 2.52
LINK ZN ZN B 80 SG CYS B 31 1555 1555 2.36
SITE 1 AC1 4 CYS B 14 CYS B 17 CYS B 38 CYS B 41
SITE 1 AC2 4 CYS B 31 CYS B 33 CYS B 53 CYS B 56
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