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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PCAF BROMODOMAIN IN COMPLEX WITH FRAGMENT ZB1916 (FRAGMENT 10)
 
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 :  1.77
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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
15WZ1Ligand/Ion(4-AZANYLPIPERIDIN-1-YL)-CYCLOPROPYL-METHANONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO10Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
15WZ1Ligand/Ion(4-AZANYLPIPERIDIN-1-YL)-CYCLOPROPYL-METHANONE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3EDO8Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
15WZ-1Ligand/Ion(4-AZANYLPIPERIDIN-1-YL)-CYCLOPROPYL-METHANONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:725 , TYR A:729 , ARG A:780 , HOH A:1021binding site for residue EDO A 901
02AC2SOFTWARELYS A:740 , HIS A:742 , GLN A:743 , ALA A:745 , TRP A:746 , MET A:749 , HOH A:1001 , HOH A:1010 , HOH A:1065binding site for residue EDO A 902
03AC3SOFTWARESER A:807 , GLU A:808binding site for residue EDO A 903
04AC4SOFTWAREVAL A:752 , LYS A:753 , ARG A:754 , EDO A:905 , HOH A:1022binding site for residue EDO A 904
05AC5SOFTWARETYR A:761 , EDO A:904 , HOH A:1056 , HOH A:1069binding site for residue EDO A 905
06AC6SOFTWAREGLU A:801 , GLN B:793binding site for residue EDO A 906
07AC7SOFTWAREPRO A:747 , THR A:755 , GLU A:756 , TYR A:809 , 5WZ A:909 , HOH A:1004 , HOH A:1089binding site for residue EDO A 907
08AC8SOFTWAREGLN A:738 , LYS A:823 , HOH A:1026 , HOH A:1048 , GLN B:743 , TRP B:746binding site for residue EDO A 908
09AC9SOFTWAREPRO A:747 , PHE A:748 , GLU A:756 , ALA A:757 , TYR A:802 , ASN A:803 , TYR A:809 , EDO A:907 , HOH A:1015 , HOH A:1017 , HOH A:1073binding site for residue 5WZ A 909
10AD1SOFTWARELYS B:733 , LEU B:736 , GLN B:737 , LYS B:740 , SER B:774 , HOH B:1015 , HOH B:1016binding site for residue EDO B 901
11AD2SOFTWAREGLN B:737 , GLN B:738 , SER B:741binding site for residue EDO B 902
12AD3SOFTWAREASN B:803 , TYR B:809 , HOH B:1001binding site for residue DMS B 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FE6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FE6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FE6)

(-) Exons   (0, 0)

(no "Exon" information available for 5FE6)

(-) 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:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5fe6 A 723 RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID 831
                                   732       742       752       762       772       782       792       802       812       822         


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 5fe6 B 722 PRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID 831
                                   731       741       751       761       771       781       791       801       811       821       831
   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 5FE6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FE6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FE6)

(-) Gene Ontology  (59, 59)

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  5fe6
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  KAT2B_HUMAN | Q92831
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  2.3.1.48
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 Related Entries

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UniProtKB/Swiss-Prot
        KAT2B_HUMAN | Q92831: 1cm0 1jm4 1n72 1wug 1wum 1zs5 2rnw 2rnx 3gg3 4nsq 5fdz 5fe0 5fe1 5fe2 5fe3 5fe4 5fe5 5fe7 5fe8 5fe9 5lvq 5lvr

(-) Related Entries Specified in the PDB File

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