3VK7 Hydrolase Dna date Nov 10, 2011
title Crystal Structure Of Dna-Glycosylase Bound To Dna Containing Hydroxyuracil
authors K.Imamura, A.Averill, S.S.Wallace, S.Doublie
compound source
Molecule: Probable Formamidopyrimidine-Dna Glycosylase
Chain: A, B
Synonym: Fapy-Dna Glycosylase, Dna-(Apurinic Or Apyrimidini Lyase, Ap Lyase;
Ec: 3.2.2.23, 4.2.99.18
Engineered: Yes
Mutation: Yes
Organism_scientific: Acanthamoeba Polyphaga Mimivirus
Organism_common: Apmv
Organism_taxid: 212035
Gene: Mimi_l315
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Dna (5'-D(Gptpapgpapcpgptpgpgpapcpg)
Chain: C, E
Engineered: Yes
Other_details: Complementary Dna

Synthetic: Yes

Molecule: Dna (5'-D(Cpgptpcpcpap(Ohu)Pgptpcptpa
Chain: D, F
Engineered: Yes
Other_details: Dna Containing 5-Hydroxyuracil

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.703 121.594 81.121 90.00 95.49 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand FMT, OHU enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene MIMI
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA., Imamura K, Averill A, Wallace SS, Doublie S, J Biol Chem. 2012 Feb 3;287(6):4288-98. Epub 2011 Dec 14. PMID:22170059
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (3vk7.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (3vk7.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 3VK7
  • CSU: Contacts of Structural Units for 3VK7
  • Structure Factors (408 Kb)
  • Retrieve 3VK7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VK7 from S2C, [Save to disk]
  • Re-refined 3vk7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VK7 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 3VK7
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3VK7, from MSDmotif at EBI
  • Fold representative 3vk7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vk7_C] [3vk7_A] [3vk7_E] [3vk7_F] [3vk7] [3vk7_D] [3vk7_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3VK7: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 3VK7
  • Community annotation for 3VK7 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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