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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CBP BROMODOMAIN IN COMPLEX WITH CPI703
 
Authors :  J. W. Setser, F. Poy, S. F. Bellon
Date :  21 Aug 15  (Deposition) - 20 Apr 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Bromodomain, Inhibitor, Epigenetics, Chromatin, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ghosh, A. Taylor, M. Chin, H. R. Huang, A. R. Conery, J. A. Mertz, A. Salmeron, P. J. Dakle, D. Mele, A. Cote, H. Jayaram, J. W. Setser, F. Poy, G. Hatzivassiliou, D. Dealmeida-Nagata, P. Sandy, C. Hatton, F. A. Romero, E. Chiang, T. Reimer, T. Crawford, E. Pardo, V. G. Watson, V. Tsui, A. G. Cochran, L. Zawadzke, J. C. Harmange, J. E. Audia, B. M. Bryant, R. T. Cummings, S. R. Magnuson, J. L. Grogan, S. F. Bellon, B. K. Albrecht, R. J. Sims, J. M. Lora
Regulatory T Cell Modulation By Cbp/Ep300 Bromodomain Inhibition.
J. Biol. Chem. V. 291 13014 2016
PubMed-ID: 27056325  |  Reference-DOI: 10.1074/JBC.M115.708560

(-) Compounds

Molecule 1 - CREB-BINDING PROTEIN
    Chains: A, B, C
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BROMODOMAIN (UNP RESIDUES 1082-1197)
    Gene: CREBBP, CBP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
158N3Ligand/Ion(4R)-6-(1-TERT-BUTYL-1H-PYRAZOL-4-YL)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
158N1Ligand/Ion(4R)-6-(1-TERT-BUTYL-1H-PYRAZOL-4-YL)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
158N1Ligand/Ion(4R)-6-(1-TERT-BUTYL-1H-PYRAZOL-4-YL)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
158N1Ligand/Ion(4R)-6-(1-TERT-BUTYL-1H-PYRAZOL-4-YL)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:1109 , PRO A:1110 , VAL A:1115 , LEU A:1120 , ASN A:1168 , VAL A:1174 , HOH A:1331binding site for residue 58N A 1201
2AC2SOFTWAREPRO B:1110 , VAL B:1115 , LEU B:1120 , TYR B:1125 , ASN B:1168 , HOH B:1318 , HOH B:1325binding site for residue 58N B 1201
3AC3SOFTWAREGLN A:1148 , LEU C:1109 , PRO C:1110 , VAL C:1115 , LEU C:1120 , ASN C:1168 , HOH C:1347binding site for residue 58N C 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DBM)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:1105 -Pro A:1106
2Asp B:1105 -Pro B:1106
3Asp C:1105 -Pro C:1106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DBM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DBM)

(-) Exons   (0, 0)

(no "Exon" information available for 5DBM)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:114
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh....hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                5dbm A 1083 KIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 1196
                                  1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192    


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                5dbm B 1084 IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 1196
                                  1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193   


Chain C from PDB  Type:PROTEIN  Length:118
                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh....hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                5dbm C 1080 GSKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG 1197
                                  1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DBM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DBM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DBM)

(-) Gene Ontology  (66, 66)

Asymmetric Unit(hide GO term definitions)

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  CBP_HUMAN | Q92793
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  2.3.1.48
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CBP_HUMAN | Q92793: 1jsp 1liq 1rdt 1wo3 1wo4 1wo5 1wo6 1wo7 1zoq 2d82 2kje 2kwf 2l84 2l85 2lxs 2lxt 2n1a 2rny 3dwy 3p1c 3p1d 3p1e 3p1f 3svh 4a9k 4n3w 4n4f 4nr4 4nr5 4nr6 4nr7 4nyv 4nyw 4nyx 4ouf 4tqn 4ts8 4whu 4yk0 5cgp 5eic 5eng 5ep7 5gh9 5h85 5i83 5i86 5i89 5i8b 5i8g 5j0d 5jem 5ktu 5ktw 5ktx 5mpz 5mqe 5mqg 5mqk 5tb6

(-) Related Entries Specified in the PDB File

4yk0