1VRL Hydrolase Dna date Mar 08, 2005
title Muty Adenine Glycosylase In Complex With Dna And Soaked Adenine Free Base
authors J.C.Fromme, A.Banerjee, S.J.Huang, G.L.Verdine
compound source
Molecule: 5'-D(Apapgpapcp(8og)Ptpgpgpapc)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Tpgptpcpcpap(Hpd)Pgptpcpt)-3'
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Muty
Chain: A
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Muty
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.278
length a length b length c angle alpha angle beta angle gamma
37.977 85.730 141.635 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 8OG, ADE, CA, HPD, SF4 enzyme Hydrolase E.C.3.2.2 BRENDA
note 1VRL supersedes 1RRT
related structures by homologous chain: 1RRS

Primary referenceStructural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase., Fromme JC, Banerjee A, Huang SJ, Verdine GL, Nature 2004 Feb 12;427(6975):652-6. PMID:14961129
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1vrl.pdb1.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 1VRL
  • CSU: Contacts of Structural Units for 1VRL
  • Likely Quarternary Molecular Structure file(s) for 1VRL
  • Retrieve 1VRL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VRL from S2C, [Save to disk]
  • View 1VRL 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 1VRL
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1VRL, from MSDmotif at EBI
  • Fold representative 1vrl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vrl_C] [1vrl_A] [1vrl_B] [1vrl]
  • SWISS-PROT database: [P83847]
  • Domain organization of [P83847_BACST] by SWISSPFAM
  • Domains found in 1VRL: [ENDO3c] [FES ] by SMART
  • Other resources with information on 1VRL
  • Community annotation for 1VRL 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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