1YQL Hydrolase Dna date Feb 02, 2005
title Catalytically Inactive Hogg1 Crosslinked With 7-Deaza-8- Azaguanine Containing Dna
authors A.Banerjee, W.Yang, M.Karplus, G.L.Verdine
compound source
Molecule: 5'-D(Pgpgptpapgpapcpcptpgpgpapc)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Pgptpcpcpap(Ppw)Pgptpcptpapc)- 3';
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: N-Glycosylasedna Lyase
Chain: A
Fragment: 8-Oxoguanine Dna Glycosylase
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ogg1, Mmh, Mutm, Ogh1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl-21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-30a
symmetry Space Group: P 65 2 2
R_factor 0.213 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
92.322 92.322 210.744 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, PPW enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 1FN7, 1YQK

Primary referenceStructure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA., Banerjee A, Yang W, Karplus M, Verdine GL, Nature. 2005 Mar 31;434(7033):612-8. PMID:15800616
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (1yql.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 1YQL
  • CSU: Contacts of Structural Units for 1YQL
  • Likely Quarternary Molecular Structure file(s) for 1YQL
  • Structure Factors (128 Kb)
  • Retrieve 1YQL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YQL from S2C, [Save to disk]
  • Re-refined 1yql structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YQL 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 1YQL
  • 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 1YQL, from MSDmotif at EBI
  • Fold representative 1yql from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yql_B] [1yql] [1yql_C] [1yql_A]
  • SWISS-PROT database: [O15527]
  • Domain organization of [OGG1_HUMAN] by SWISSPFAM
  • Domain found in 1YQL: [ENDO3c ] by SMART
  • Other resources with information on 1YQL
  • Community annotation for 1YQL 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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