3C58 Hydrolase Dna date Jan 31, 2008
title Crystal Structure Of A Complex Between The Wild-Type Lactoco Lactis Fpg (Mutm) And A N7-Benzyl-Fapy-Dg Containing Dna
authors F.Coste, B.Castaing, T.Carell
compound source
Molecule: Dna Glycosylase
Chain: A
Synonym: Fapy-Dna Glycosylase, Dna-Apurinic Or Apyrimidinic Lyase Mutm, Ap Lyase Mutm;
Ec: 4.2.99.18
Engineered: Yes
Organism_scientific: Lactococcus Lactis
Organism_taxid: 416870
Variant: Subsp. Cremoris
Gene: Mutm, Fpg
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-C

Molecule: Dna (5'-D(Dcpdtpdcpdtpdtpdtp(Sos) Pdtpdtpdtpdcpdtpdcpdg)-3');
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna (5'- D(Dgpdcpdgpdapdgpdapdapdapdcpdapdapdapdgpda)-
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 41 21 2
R_factor 0.172 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.356 91.356 140.943 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL, SOS, ZN enzyme Lyase E.C.4.2.99.18 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceBacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode., Coste F, Ober M, Le Bihan YV, Izquierdo MA, Hervouet N, Mueller H, Carell T, Castaing B, Chem Biol. 2008 Jul 21;15(7):706-17. PMID:18635007
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (68 Kb) [Save to disk]
  • Biological Unit Coordinates (3c58.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 3C58
  • CSU: Contacts of Structural Units for 3C58
  • Likely Quarternary Molecular Structure file(s) for 3C58
  • Structure Factors (726 Kb)
  • Retrieve 3C58 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C58 from S2C, [Save to disk]
  • Re-refined 3c58 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C58 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 3C58
  • 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 3C58, from MSDmotif at EBI
  • Fold representative 3c58 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c58_B] [3c58_C] [3c58] [3c58_A]
  • SWISS-PROT database: [P42371]
  • Domain organization of [FPG_LACLC] by SWISSPFAM
  • Domains found in 3C58: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 3C58
  • Community annotation for 3C58 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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