1L2D Hydrolase Dna date Feb 20, 2002
title Mutm (Fpg)-Dna Estranged Guanine Mismatch Recognition Complex
authors J.C.Fromme, G.L.Verdine
compound source
Molecule: 5'- D(Apggptpapgpapcpgptpgpgpapcpgpc)-3';
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Tpgpcgptpcpcpap(Hpd) Pgptpcptpapcpc)-3';
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Mutm
Chain: A
Synonym: Fpg
Engineered: Yes

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Mutm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.217 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.906 94.486 104.384 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand HPD, ZN enzyme
related structures by homologous chain: 1L1T, 1L2C
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM., Fromme JC, Verdine GL, Nat Struct Biol 2002 Jul;9(7):544-52. PMID:12055620
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (1l2d.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 1L2D
  • CSU: Contacts of Structural Units for 1L2D
  • Likely Quarternary Molecular Structure file(s) for 1L2D
  • Structure Factors (228 Kb)
  • Retrieve 1L2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L2D from S2C, [Save to disk]
  • Re-refined 1l2d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1L2D 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 1L2D
  • 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 1L2D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l2da1, region A:135-220 [Jmol] [rasmolscript] [script source]
        - Domain d1l2da2, region A:2-134 [Jmol] [rasmolscript] [script source]
        - Domain d1l2da3, region A:235-274 [Jmol] [rasmolscript] [script source]
  • Fold representative 1l2d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1l2d_C] [1l2d] [1l2d_B] [1l2d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1L2D: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 1L2D
  • Community annotation for 1L2D 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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