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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CBP BROMODOMAIN IN COMPLEX WITH CPI098
 
Authors :  S. F. Bellon, H. Jayaram
Date :  03 Mar 15  (Deposition) - 20 Apr 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Cbp, Cpi098, Transferase (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, D
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN
    Gene: CREBBP, CBP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1984Ligand/Ion(4R)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
198-1Ligand/Ion(4R)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
198-1Ligand/Ion(4R)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
198-1Ligand/Ion(4R)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
198-1Ligand/Ion(4R)-4-METHYL-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:1110 , VAL A:1115 , ASN A:1168 , HOH A:1318binding site for residue 98 A 1201
2AC2SOFTWAREPRO A:1123 , ASP A:1124 , ARG B:1169 , THR B:1171 , SER B:1172binding site for residue EDO A 1202
3AC3SOFTWAREPRO B:1110 , VAL B:1115 , ASN B:1168 , HOH B:1308binding site for residue 98 B 1201
4AC4SOFTWAREPRO C:1110 , VAL C:1115 , TYR C:1125 , TYR C:1167 , ASN C:1168 , HOH C:1308binding site for residue 98 C 1201
5AC5SOFTWAREPRO D:1110 , VAL D:1115 , TYR D:1125 , ASN D:1168 , VAL D:1174 , HOH D:1303binding site for residue 98 D 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YK0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:1105 -Pro A:1106
2Asp B:1105 -Pro B:1106
3Asp C:1105 -Pro C:1106
4Asp D:1105 -Pro D:1106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YK0)

(-) Exons   (0, 0)

(no "Exon" information available for 4YK0)

(-) 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: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
                4yk0 A 1084 IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 1196
                                  1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193   


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..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                4yk0 B 1084 IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 1196
                                  1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193   


Chain C from PDB  Type:PROTEIN  Length:99
                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                4yk0 C 1089 ELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEI 1189
                                  1098      1108      1118      1128      1138      1150      1160      1170      1180         
                                                                                   1147|                                       
                                                                                    1150                                       


Chain D from PDB  Type:PROTEIN  Length:91
                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                4yk0 D 1095 MPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQ 1187
                                  1104      1114      1124      1134      1144  ||  1156      1166      1176      1186 
                                                                             1147|                                     
                                                                              1150
   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 4YK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YK0)

(-) Gene Ontology  (66, 66)

Asymmetric Unit(hide GO term definitions)

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  4yk0
    Family and Domain Information: ProDom | SYSTERS
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  CBP_HUMAN | Q92793
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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 5cgp 5dbm 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

(no "Related Entries Specified in the PDB File" available for 4YK0)