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 NSD3 TANDEM PHD5-C5HCH DOMAINS COMPLEXED WITH H3 PEPTIDE 1-15
 
Authors :  F. Li, C. He, J. Wu, Y. Shi
Date :  17 Aug 12  (Deposition) - 02 Jan 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Zinc Finger, Transcription, Histone, Nuclear Protein, Transferase- Nuclear Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. He, F. Li, J. Zhang, J. Wu, Y. Shi
The Methyltransferase Nsd3 Has Chromatin-Binding Motifs, Phd5-C5Hch, That Are Distinct From Other Nsd (Nuclear Receptor Set Domain) Family Members In Their Histone H3 Recognition.
J. Biol. Chem. V. 288 4692 2013
PubMed-ID: 23269674  |  Reference-DOI: 10.1074/JBC.M112.426148

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE NSD3
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1310-1413
    Gene: WHSC1L1, NSD3, DC28
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR SET DOMAIN-CONTAINING PROTEIN 3, PROTEIN WHISTLE, WHSC1-LIKE 1 ISOFORM 9 WITH METHYLTRANSFERASE ACTIVITY TO LYSINE, WOLF-HIRSCHHORN SYNDROME CANDIDATE 1-LIKE PROTEIN 1, WHSC1-LIKE PROTEIN 1
 
Molecule 2 - HISTONE H3.3
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 2-16
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1324 , CYS A:1327 , HIS A:1346 , CYS A:1349BINDING SITE FOR RESIDUE ZN A 1501
2AC2SOFTWARECYS A:1336 , CYS A:1341 , CYS A:1362 , HIS A:1365BINDING SITE FOR RESIDUE ZN A 1502
3AC3SOFTWARECYS A:1378 , CYS A:1381 , CYS A:1405 , HIS A:1408BINDING SITE FOR RESIDUE ZN A 1503
4AC4SOFTWARECYS A:1367 , CYS A:1370 , CYS A:1386 , HIS A:1389BINDING SITE FOR RESIDUE ZN A 1504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GNF)

(-) 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:96
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeee........ee.hhhhh..........hhhhh.........ee......ee.........ee......ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                4gnf A 1318 QMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP 1413
                                  1327      1337      1347      1357      1367      1377      1387      1397      1407      


Chain C from PDB  Type:PROTEIN  Length:9
                                          
               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
                4gnf C    1 ARTKQTARK    9
   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 4GNF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 43)

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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gnf)
 

(-) 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
  4gnf
    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
  NSD3_HUMAN | Q9BZ95
    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)
  NSD3_HUMAN | Q9BZ95
    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 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 5jlb 5kdm 5x7x
        NSD3_HUMAN | Q9BZ95: 2daq 2ncz 2nd1 4gnd 4gne 4gng 4rxj 5upd

(-) Related Entries Specified in the PDB File

4gnd 4gne 4gng