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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PCAF BROMODOMAIN IN COMPLEX WITH FRAGMENT MB364 (FRAGMENT 5)
 
Authors :  A. Chaikuad, F. Von Delft, C. Bountra, C. H. Arrowsmith, A. M. Edwards, Structural Genomics Consortium (Sgc)
Date :  16 Dec 15  (Deposition) - 13 Jan 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Signaling Protein, Bromodomain, Histone Acetyltransferase Kat2B, Histone, Acetylation, Acetyllysine, Epigenetics, Structural Genomics Consortium (Sgc) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, S. Lang, P. E. Brennan, C. Temperini, O. Fedorov, J. Hollander, R. Nachane, C. Abell, S. Muller, G. Siegal, S. Knapp
Structure-Based Identification Of Inhibitory Fragments Targeting The P300/Cbp-Associated Factor Bromodomain.
J. Med. Chem. V. 59 1648 2016
PubMed-ID: 26731131  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01719

(-) Compounds

Molecule 1 - HISTONE ACETYLTRANSFERASE KAT2B
    Chains: A, B
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28-BSA4
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Expression System Vector Type: PLASMID
    Fragment: PCAF BROMODOMAIN, UNP RESIDUES 715-831
    Gene: KAT2B, PCAF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE ACETYLTRANSFERASE PCAF,HISTONE ACETYLASE PCAF,LYSINE ACETYLTRANSFERASE 2B,P300/CBP-ASSOCIATED FACTOR,P/CAF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
15WY2Ligand/Ion2,3-DIHYDRO-1,4-BENZODIOXINE-5-CARBOXAMIDE
2EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
15WY1Ligand/Ion2,3-DIHYDRO-1,4-BENZODIOXINE-5-CARBOXAMIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
15WY1Ligand/Ion2,3-DIHYDRO-1,4-BENZODIOXINE-5-CARBOXAMIDE
2EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:818 , PRO B:805 , GLU B:806 , TYR B:810 , LYS B:811 , EDO B:901 , HOH B:1035binding site for residue EDO A 901
2AC2SOFTWAREVAL A:752 , TYR A:761binding site for residue EDO A 902
3AC3SOFTWAREPRO A:747 , GLU A:756 , ASN A:803 , TYR A:809 , HOH A:1005binding site for residue 5WY A 903
4AC4SOFTWARELYS A:818 , EDO A:901 , GLU B:806 , HOH B:1011binding site for residue EDO B 901
5AC5SOFTWARELYS B:733 , LEU B:736 , GLN B:737 , SER B:774 , HOH B:1006binding site for residue EDO B 902
6AC6SOFTWAREARG A:776 , HOH A:1080 , TYR B:729 , LYS B:778 , HOH B:1002binding site for residue EDO B 903
7AC7SOFTWAREGLN A:737 , PRO B:747 , GLU B:756 , ASN B:803 , TYR B:809 , HOH B:1004binding site for residue 5WY B 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FE4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FE4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FE4)

(-) Exons   (0, 0)

(no "Exon" information available for 5FE4)

(-) 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:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5fe4 A 724 DPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID 831
                                   733       743       753       763       773       783       793       803       813       823        


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5fe4 B 724 DPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID 831
                                   733       743       753       763       773       783       793       803       813       823
   Legend:   → Mismatch (orange background)
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  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 5FE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FE4)

(-) Gene Ontology  (59, 59)

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  KAT2B_HUMAN | Q92831
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 Related Entries

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

UniProtKB/Swiss-Prot
        KAT2B_HUMAN | Q92831: 1cm0 1jm4 1n72 1wug 1wum 1zs5 2rnw 2rnx 3gg3 4nsq 5fdz 5fe0 5fe1 5fe2 5fe3 5fe5 5fe6 5fe7 5fe8 5fe9 5lvq 5lvr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FE4)