3VNN Ligase date Jan 17, 2012
title Crystal Structure Of A Sub-Domain Of The Nucleotidyltransfer (Adenylation) Domain Of Human Dna Ligase Iv
authors T.Ochi, Q.Wu, D.Y.Chirgadze, J.G.Grossmann, V.M.Bolanos-Garcia, T.L.Blundell
compound source
Molecule: Dna Ligase 4
Chain: A
Fragment: A Sub-Domain Of The Nucleotidyltransferase (Adeny Domain, Unp Residues 268-405;
Synonym: Dna Ligase Iv, Polydeoxyribonucleotide Synthase [A
Ec: 6.5.1.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lig4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phat5
symmetry Space Group: P 41 2 2
R_factor 0.273 R_Free 0.305
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.086 39.086 197.393 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand
enzyme Ligase E.C.6.5.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Insights into the Role of Domain Flexibility in Human DNA Ligase IV., Ochi T, Wu Q, Chirgadze DY, Grossmann JG, Bolanos-Garcia VM, Blundell TL, Structure. 2012 May 31. PMID:22658747
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (3vnn.pdb1.gz) 42 Kb
  • CSU: Contacts of Structural Units for 3VNN
  • Structure Factors (58 Kb)
  • Retrieve 3VNN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VNN from S2C, [Save to disk]
  • Re-refined 3vnn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VNN 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 3VNN
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3VNN, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vnn] [3vnn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VNN
  • Community annotation for 3VNN at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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