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

(-) Description

Title :  CRYSTAL STRUCTURE OF BRD9 BROMODOMAIN BOUND TO A CROTONYLLYSINE PEPTIDE
 
Authors :  Y. Tang, S. Bellon, A. G. Cochran, F. Poy
Date :  23 Mar 15  (Deposition) - 16 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B,Y,Z
Biol. Unit 1:  A,Z  (1x)
Biol. Unit 2:  B,Y  (1x)
Keywords :  Bromodomain-Crotonyllysine Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. M. Flynn, O. W. Huang, F. Poy, M. Oppikofer, S. F. Bellon, Y. Tang, A. G. Cochran
A Subset Of Human Bromodomains Recognizes Butyryllysine And Crotonyllysine Histone Peptide Modifications.
Structure V. 23 1801 2015
PubMed-ID: 26365797  |  Reference-DOI: 10.1016/J.STR.2015.08.004

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 9
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPRSF
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentBROMODOMAIN (UNP RESIDUES 17-123)
    GeneBRD9, UNQ3040/PRO9856
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8, BRD9
 
Molecule 2 - HISTONE H4
    ChainsZ, Y
    EngineeredYES
    FragmentN-TERMINAL TAIL (UNP RESIDUES 2-12)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsLYSINE RESIDUES CROTONYLATED
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABYZ
Biological Unit 1 (1x)A  Z
Biological Unit 2 (1x) BY 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1KCR2Mod. Amino AcidN-6-CROTONYL-L-LYSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1KCR1Mod. Amino AcidN-6-CROTONYL-L-LYSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1KCR1Mod. Amino AcidN-6-CROTONYL-L-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 4YYH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YYH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YYH)

(-) 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:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4yyh A  22 STPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSK 123
                                    31        41        51        61        71        81        91       101       111       121  

Chain B from PDB  Type:PROTEIN  Length:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4yyh B  21 ESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSK 123
                                    30        40        50        60        70        80        90       100       110       120   

Chain Y from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4yyh Y   6 GGkG   9
                              | 
                              8-KCR

Chain Z from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4yyh Z   6 GGkG   9
                              | 
                              | 
                              8-KCR

   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 4YYH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 38)

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
    KCR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4yyh)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4yyh)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4yyh
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BRD9_HUMAN | Q9H8M2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  H4_HUMAN | P62805
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  BRD9_HUMAN | Q9H8M2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  H4_HUMAN | P62805
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BRD9_HUMAN | Q9H8M23hme 4nqn 4uit 4uiu 4uiv 4uiw 4xy8 4yy4 4yy6 4yyd 4yyg 4yyi 4yyj 4yyk 4z6h 4z6i 5e9v 5eu1 5f1h 5f1l 5f25 5f2p 5i40 5i7x 5i7y 5igm 5ign 5ji8
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x

(-) Related Entries Specified in the PDB File

4yy4 4yy6 4yyd 4yyg 4yyi 4yyj 4yyk 4yym 4yyn