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(-) Description

Title :  CRYSTAL STRUCTURE OF THE WHSC1 PWWP1 DOMAIN
 
Authors :  S. Qin, W. Tempel, A. Dong, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M J. Min, Structural Genomics Consortium (Sgc)
Date :  31 Mar 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,W,X,Y,Z
Keywords :  Pwwp Domain, Structural Genomics Consortium, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Qin, W. Tempel, A. Dong, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min
Crystal Structure Of The Whsc1 Pwwp1 Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE NSD2
    Chains: A, B
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MULTIPLE MYELOMA SET DOMAIN-CONTAINING PROTEIN,MMSET,NUCLEAR SET DOMAIN-CONTAINING PROTEIN 2,PROTEIN TRITHORAX-5,WOLF-HIRSCHHORN SYNDROME CANDIDATE 1 PROTEIN
 
Molecule 2 - DODECA-2-DEOXY-NUCLEOTIDE, POORLY RESOLVED BY ELECTRON DENSITY
    Chains: W, X, Y
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*TP*(DN))-3')
    Chains: Z
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: INTERPRETATION OF WEAK ELECTRON DENSITY IN TERMS OF AN UNIDENTIFIED FRAGMENT OF THE DODECADEOXYNUCLEOTIDE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABWXYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 46)

Asymmetric/Biological Unit (3, 46)
No.NameCountTypeFull Name
1DN1Mod. ResidueUNKNOWN 2'-DEOXYNUCLEOTIDE
2MSE6Mod. Amino AcidSELENOMETHIONINE
3UNX39Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:316 , ARG A:319 , DG W:3 , DA W:4 , DC Z:0binding site for Di-nucleotide DT Z 1 and DN Z 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5VC8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VC8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VC8)

(-) Exons   (0, 0)

(no "Exon" information available for 5VC8)

(-) 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:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee.......eeeee.........ee....eeeeee......eeeee...eee..hhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vc8 A 216 HLLKYNVGDLVWSKVSGYPWWPCmVSADPLLHSYTKLKARQYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEmGIVQAEEAASmSVEERKAKFTF 346
                                   225       235   |   245       260       270       280       290       300       310       320   |   330    |  340      
                                                 239-MSE       253|                                                              324-MSE    335-MSE       
                                                                259                                                                                       


Chain B from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.......eeeee.........eee.hhh...eeeeeee......eeeee...eee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vc8 B 217 LLKYNVGDLVWSKVSGYPWWPCmVSADPLLHSYTKLKGQKKSARQYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQALLKPISGKLRAQWEmGIVQAEEAASmSVEERKAKFTFLYVG 350
                                   226       236  |    246       256       266       276       286       296    || 314       324       334|      344      
                                                239-MSE                                                       301|           324-MSE    335-MSE           
                                                                                                               310                                        


Chain W from PDB  Type:DNA  Length:12
                                            
                 5vc8 W   1 GAGATCGATCTC  12
                                    10  


Chain X from PDB  Type:DNA  Length:12
                                            
                 5vc8 X   1 GAGATCGATCTC  12
                                    10  


Chain Y from PDB  Type:DNA  Length:12
                                            
                 5vc8 Y   1 GAGATCGATCTC  12
                                    10  


Chain Z from PDB  Type:DNA  Length:3
                                   
                 5vc8 Z   0 CTx   2
                              |
                              2-DN
   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 5VC8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VC8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VC8)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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