4NRW Hydrolase, Lyase Dna date Nov 27, 2013
title Mvnei1-G86d
authors A.Prakash, S.Doublie
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A, B
Synonym: Nei1 (Mvnei1) Dna Glycosylase, Fapy-Dna Glycosylas (Apurinic Or Apyrimidinic Site) 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: Endonuclease Viii (Nei) 1, Mimi_l315
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: 5'-D(Gptpapgpapcpcptpgpgpapcpg)-3'
Chain: C, E
Engineered: Yes
Other_details: Complementary Dna Strand

Synthetic: Yes

Molecule: 5'-D(Cpgptpcpcpap(3dr)Pgptpcptpapc)-
Chain: D, F
Engineered: Yes
Other_details: Furan-Containing Dna Strand

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.260 R_Free 0.315
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.401 121.682 79.993 90.00 95.68 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand 3DR enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene MIMI
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceGenome and cancer single nucleotide polymorphisms of the human NEIL1 DNA glycosylase: Activity, structure, and the effect of editing., Prakash A, Carroll BL, Sweasy JB, Wallace SS, Doublie S, DNA Repair (Amst). 2014 Feb;14:17-26. doi: 10.1016/j.dnarep.2013.12.003. Epub, 2013 Dec 29. PMID:24382305
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (240 Kb) [Save to disk]
  • Biological Unit Coordinates (4nrw.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (4nrw.pdb2.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 4NRW
  • CSU: Contacts of Structural Units for 4NRW
  • Structure Factors (751 Kb)
  • Retrieve 4NRW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NRW from S2C, [Save to disk]
  • Re-refined 4nrw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NRW 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 4NRW
  • 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 4NRW, from MSDmotif at EBI
  • Fold representative 4nrw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nrw_A] [4nrw] [4nrw_D] [4nrw_F] [4nrw_C] [4nrw_E] [4nrw_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4NRW: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 4NRW
  • Community annotation for 4NRW at PDBWiki (http://pdbwiki.org)

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