Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PCAF BROMODOMAIN IN COMPLEX WITH FRAGMENT ZB2216 (FRAGMENT 11)
 
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 :  2.08
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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
15WU1Ligand/Ion1-(2-HYDROXYETHYL)-3-METHYL-6,7-DIHYDRO-5~{H}-INDAZOL-4-ONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
15WU1Ligand/Ion1-(2-HYDROXYETHYL)-3-METHYL-6,7-DIHYDRO-5~{H}-INDAZOL-4-ONE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
15WU-1Ligand/Ion1-(2-HYDROXYETHYL)-3-METHYL-6,7-DIHYDRO-5~{H}-INDAZOL-4-ONE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:733 , GLN A:737 , SER A:774 , HOH A:1016binding site for residue EDO A 901
2AC2SOFTWAREPRO A:747 , VAL A:752 , LYS A:753 , GLU A:756 , ALA A:757 , TYR A:802 , ASN A:803 , TYR A:809 , HOH A:1007 , HOH A:1014binding site for residue 5WU A 902
3AC3SOFTWAREGLU A:750 , LYS B:740 , HIS B:742 , GLN B:743 , ALA B:745 , TRP B:746 , HOH B:1009 , HOH B:1028binding site for residue EDO B 901
4AC4SOFTWAREVAL B:752 , LYS B:753 , ARG B:754 , TYR B:761 , HOH B:1003 , HOH B:1030 , HOH B:1031binding site for residue EDO B 902
5AC5SOFTWAREPRO B:747 , ASN B:803 , HOH B:1011binding site for residue DMS B 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FE7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FE7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FE7)

(-) Exons   (0, 0)

(no "Exon" information available for 5FE7)

(-) 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...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5fe7 A 723 RDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID 831
                                   732       742       752       762       772       782       792       802       812       822         


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhh...hhhhh.hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5fe7 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 5FE7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FE7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FE7)

(-) Gene Ontology  (59, 59)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5WU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fe7)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5fe7
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KAT2B_HUMAN | Q92831
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.48
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KAT2B_HUMAN | Q92831
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5fe8 5fe9 5lvq 5lvr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FE7)