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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PCAF BROMODOMAIN IN COMPLEX WITH COMPOUND-E (CPD-E)
 
Authors :  A. Chaikuad, P. Filippakopoulos, F. Von Delft, C. Bountra, C. H. Arrow A. M. Edwards, A. L. Hopkins, S. Knapp, Structural Genomics Consort
Date :  14 Sep 16  (Deposition) - 26 Oct 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signaling Protein, Bromodomain, Histone Acetyltransferase Kat2B, Histone, Acetylation, Acetyllysine, Epigenetics, Structural Genomics Consortium (Sgc) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Navratilova, T. Aristotelous, S. Picaud, A. Chaikuad, S. Knapp, P. Filappakopoulos, A. L. Hopkins
Discovery Of New Bromodomain Scaffolds By Biosensor Fragmen Screening.
Acs Med Chem Lett V. 7 1213 2016
PubMed-ID: 27994766  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00154

(-) Compounds

Molecule 1 - HISTONE ACETYLTRANSFERASE KAT2B
    Chains: A, B
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Expression System Vector Type: PLASMID
    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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
178Y1Ligand/Ion5-METHYL-2-PHENYL-1,2,3-TRIAZOLE-4-CARBOXAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO6Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:733 , GLN A:737 , SER A:774 , LEU A:777 , HOH A:1004binding site for residue EDO A 901
2AC2SOFTWARETYR A:729 , LYS A:778 , ARG A:780 , ARG B:776binding site for residue EDO A 902
3AC3SOFTWAREGLN A:743 , TRP A:746 , GLU A:808 , CYS A:812 , GLN B:738 , LYS B:823 , HOH B:1039binding site for residue EDO A 903
4AC4SOFTWAREPRO A:747 , GLU A:756 , ASN A:803 , TYR A:809 , HOH A:1003 , GLN B:737binding site for residue 78Y A 904
5AC5SOFTWAREVAL B:752 , LYS B:753 , ARG B:754 , TYR B:761 , HOH B:1044binding site for residue EDO B 901
6AC6SOFTWAREGLU A:750 , LYS B:740 , HIS B:742 , GLN B:743 , ALA B:745 , TRP B:746 , MET B:749 , HOH B:1003binding site for residue EDO B 902
7AC7SOFTWAREPRO B:747 , GLU B:756 , TYR B:809 , DMS B:904binding site for residue EDO B 903
8AC8SOFTWAREPRO B:747 , ASN B:803 , EDO B:903 , HOH B:1005binding site for residue DMS B 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LVR)

(-) Sequences/Alignments

Asymmetric/Biological 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 ..hhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5lvr 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 .hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5lvr B 723 RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLI 830
                                   732       742       752       762       772       782       792       802       812       822
   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 5LVR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5fe4 5fe5 5fe6 5fe7 5fe8 5fe9 5lvq

(-) Related Entries Specified in the PDB File

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