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

(-) Description

Title :  CRYSTAL STRUCTURE OF SETD2 BOUND TO HISTONE H3.3 K36I PEPTIDE
 
Authors :  H. Li, S. Yang
Date :  26 Apr 16  (Deposition) - 02 Nov 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Set Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yang, X. Zheng, C. Lu, G. M. Li, C. D. Allis, H. Li
Molecular Basis For Oncohistone H3 Recognition By Setd2 Methyltransferase
Genes Dev. V. 30 1611 2016
PubMed-ID: 27474439  |  Reference-DOI: 10.1101/GAD.284323.116

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD2
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1434-1711
    Gene: SETD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HIF-1,HUNTINGTIN YEAST PARTNER B,HUNTINGTIN-INTERACTING PROTEIN 1,HIP-1,HUNTINGTIN-INTERACTING PROTEIN B,LYSINE N- METHYLTRANSFERASE 3A,SET DOMAIN-CONTAINING PROTEIN 2,HSET2,P231HBP
 
Molecule 2 - HISTONE H3.3
    Chains: B
    Engineered: YES
    Fragment: H3 PEPTIDE, UNP RESIDUES 30-43
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SCN3Ligand/IonTHIOCYANATE ION
4ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:1560 , GLY A:1561 , TRP A:1562 , ILE A:1602 , HIS A:1603 , TYR A:1604 , TYR A:1605 , ARG A:1625 , PHE A:1626 , ASN A:1628 , HIS A:1629 , TYR A:1666 , LYS A:1677 , CYS A:1678 , PHE A:1679 , HOH A:1935 , HOH A:1961 , HOH A:1966binding site for residue SAH A 1801
2AC2SOFTWAREHIS A:1629 , PHE A:1668 , ARG A:1686 , GLY A:1690 , GLY A:1691 , HOH A:1994 , HOH A:2096binding site for residue SCN A 1802
3AC3SOFTWARELYS A:1590binding site for residue SCN A 1803
4AC4SOFTWARETHR A:1637 , LYS A:1639 , HOH A:2058 , HIS B:39 , ARG B:40binding site for residue SCN A 1804
5AC5SOFTWAREGLU A:1477 , LYS A:1547 , LYS A:1677 , CYS A:1678 , GLY A:1687 , HOH A:1950binding site for residue GOL A 1805
6AC6SOFTWAREARG A:1509 , ASP A:1537 , CYS A:1539 , GLN A:1548 , HOH A:1927 , HOH A:2112binding site for residue GOL A 1806
7AC7SOFTWARECYS A:1499 , CYS A:1501 , CYS A:1516 , CYS A:1520binding site for residue ZN A 1807
8AC8SOFTWARECYS A:1516 , CYS A:1529 , CYS A:1533 , CYS A:1539binding site for residue ZN A 1808
9AC9SOFTWARECYS A:1631 , CYS A:1678 , CYS A:1680 , CYS A:1685binding site for residue ZN A 1809

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JLB)

(-) 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:248
                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhh.......ee....ee..............hhhhhhhh.......hhhhhh.........hhhhh............eeeee.....eeeee........eeee...eeehhhhhhhhhhhhhhh......eeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee........eeee....ee.........................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jlb A 1447 PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGK 1703
                                  1456      1466      1476      1486||    1505      1515      1525      1535      1545      1555      1565      1575      1585      1595      1605      1615      1625      1635      1645      1655      1665      1675      1685      1695        
                                                                 1487|                                                                                                                                                                                                              
                                                                  1497                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .....eee...... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                5jlb B   29 APSTGGVIKPHRYR   42
                                    38
   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 5JLB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (59, 63)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jlb)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  5jlb
    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
  H33_HUMAN | P84243
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SETD2_HUMAN | Q9BYW2
    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)
  2.1.1.43
    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
  H33_HUMAN | P84243
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SETD2_HUMAN | Q9BYW2
    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
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5kdm 5x7x
        SETD2_HUMAN | Q9BYW2: 2a7o 2mdc 2mdi 2mdj 4fmu 4h12 5jjy 5jle 5lss 5lsx 5lsy 5lsz 5lt6 5lt7 5lt8 5v21 5v22

(-) Related Entries Specified in the PDB File

5jjy 5jle