3LQC	Dna-Binding Protein	date	Feb 09, 2010
title	X-Ray Crystal Structure Of Oxidized Xrcc1 Bound To Dna Pol B Thumb Domain
authors	M.J.Cuneo, J.M.Krahn, R.E.London
compound		source
Molecule: Dna Repair Protein Xrcc1 Chain: A Synonym: X-Ray Repair Cross-Complementing Protein 1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Strain: Homo Sapiens Gene: Xrcc1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21a
Molecule: Dna Polymerase Beta Chain: B Ec: 2.7.7.7, 4.2.99.- Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Rat Organism_taxid: 10116 Gene: Polb Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21a
symmetry	Space Group: P 31 2 1	R_factor 0.189 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.240 75.240 126.160 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.35 Å
ligand	CO3, NA	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component B DNA binding damaged DNA binding catalytic activity DNA-directed DNA polymerase ... protein binding microtubule binding transferase activity nucleotidyltransferase activ... lyase activity enzyme binding metal ion binding DNA replication DNA repair base-excision repair pyrimidine dimer repair response to DNA damage stimu... cell death negative regulation of apopt... response to ethanol nucleus cytoplasm microtubule spindle microtubule
Primary reference	Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity., Cuneo MJ, London RE, Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6805-10. Epub 2010 Mar 29. PMID:20351257

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk] Biological Unit Coordinates (3lqc.pdb1.gz) 61 Kb LPC: Ligand-Protein Contacts for 3LQC CSU: Contacts of Structural Units for 3LQC Structure Factors (138 Kb) Retrieve 3LQC in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3LQC from S2C, [Save to disk] Re-refined 3lqc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3LQC 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3LQC

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 3LQC, from MSDmotif at EBI Fold representative 3lqc from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3lqc_A] [3lqc_B] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3LQC with the sequences similar proteins can be viewed for 3LQC's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3LQC

Community annotation for 3LQC at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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