1YQM	Hydrolase Dna	date	Feb 02, 2005
title	Catalytically Inactive Human 8-Oxoguanine Glycosylase Crossl 7-Deazaguanine 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(7gu)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: Pet30-A
symmetry	Space Group: P 65 2 2	R_factor 0.212 R_Free 0.261
crystal cell	length a length b length c angle alpha angle beta angle gamma 92.508 92.508 210.649 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	7GU, CA	enzyme	Hydrolase E.C.3.2.2 BRENDA
related structures	by homologous chain: 1YQK, 1YQR
Gene Ontology	Chain Function Process Component A
Primary reference	Structure 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] (66 Kb) [Save to disk] Biological Unit Coordinates (1yqm.pdb1.gz) 61 Kb LPC: Ligand-Protein Contacts for 1YQM CSU: Contacts of Structural Units for 1YQM Likely Quarternary Molecular Structure file(s) for 1YQM Structure Factors (146 Kb) Retrieve 1YQM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YQM from S2C, [Save to disk] Re-refined 1yqm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YQM 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 1YQM

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 3D motif for 1YQM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1yqm_C] [1yqm_B] [1yqm] [1yqm_A] SWISS-PROT database: [O15527] Domain organization of [OGG1_HUMAN] by SWISSPFAM Domain found in 1YQM: [ENDO3c ] by SMART

Other resources with information on 1YQM

Community annotation for 1YQM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---