3A46 Hydrolase date Jul 01, 2009
title Crystal Structure Of Mvnei1thf Complex
authors K.Imamura, S.Wallace, S.Doublie
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A, B
Synonym: Fapy-Dna Glycosylase, Dna-(Apurinic Or Apyrimidini Lyase, Ap Lyase, Endonuclease Viii, Mvnei1;
Engineered: Yes
Organism_scientific: Acanthamoeba Polyphaga Mimivirus
Organism_common: Apmv
Organism_taxid: 212035
Gene: 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
Chain: C, E
Engineered: Yes

Synthetic: Yes
Other_details: Nucleotide Synthesis

Molecule: Dna
Chain: D, F
Engineered: Yes

Synthetic: Yes
Other_details: Nucleotide Synthesis
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
39.513 121.462 80.510 90.00 95.50 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 3DR, GOL enzyme Hydrolase E.C. BRENDA
A, B

Primary referenceStructural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA., Imamura K, Wallace SS, Doublie S, J Biol Chem. 2009 Jul 22. PMID:19625256
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (3a46.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3a46.pdb2.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 3A46
  • CSU: Contacts of Structural Units for 3A46
  • Likely Quarternary Molecular Structure file(s) for 3A46
  • Structure Factors (225 Kb)
  • Retrieve 3A46 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A46 from S2C, [Save to disk]
  • Re-refined 3a46 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A46 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 3A46
  • 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 3A46, from MSDmotif at EBI
  • Fold representative 3a46 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a46_B] [3a46] [3a46_D] [3a46_E] [3a46_C] [3a46_F] [3a46_A]
  • SWISS-PROT database: [Q5UQ00]
  • Domain organization of [FPG_MIMIV] by SWISSPFAM
  • Domains found in 3A46: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 3A46
  • Community annotation for 3A46 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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