5VC8 Dna Binding Protein date Mar 31, 2017
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)
compound source
Molecule: Histone-Lysine N-Methyltransferase Nsd2
Chain: A, B
Synonym: Multiple Myeloma Set Domain-Containing Protein,Mms Set Domain-Containing Protein 2,Protein Trithorax-5,Wolf-Hi Syndrome Candidate 1 Protein;
Ec: 2.1.1.43
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nsd2, Kiaa1090, Mmset, Trx5, Whsc1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-V2r-Prare2
Expression_system_plasmid: Pet28-Mhl

Molecule: Dodeca-2-Deoxy-Nucleotide, Poorly Resolved By Ele Density;
Chain: W, X, Y
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pcptp(Dn))-3')
Chain: Z
Engineered: Yes
Other_details: Interpretation Of Weak Electron Density In T Unidentified Fragment Of The Dodecadeoxynucleotide.
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.200 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.990 82.990 115.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand DN, MSE, UNX enzyme Transferase E.C.2.1.1.43 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (5vc8.pdb1.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 5VC8
  • CSU: Contacts of Structural Units for 5VC8
  • Structure Factors (7141 Kb)
  • Retrieve 5VC8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VC8 from S2C, [Save to disk]
  • Re-refined 5vc8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VC8 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5VC8
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vc8_B] [5vc8_W] [5vc8_X] [5vc8_A] [5vc8_Z] [5vc8_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VC8
  • Community annotation for 5VC8 at PDBWiki (http://pdbwiki.org)

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