1L2B Hydrolase Dna date Feb 20, 2002
title Mutm (Fpg) Dna End-Product Structure
authors J.C.Fromme, G.L.Verdine
compound source
Molecule: 5'-D(Apgpgptpapgpapcpcptpgpgpapcpg
Chain: B
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-D(Tpgpcpgptpcpc(Ad2))-3'
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Pgptpcptpapcpc)-3'
Chain: D
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 0.209 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.179 94.518 105.004 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand AD2, ZN enzyme
related structures by homologous chain: 1R2Y
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] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1l2b.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1L2B
  • CSU: Contacts of Structural Units for 1L2B
  • Likely Quarternary Molecular Structure file(s) for 1L2B
  • Structure Factors (117 Kb)
  • Retrieve 1L2B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L2B from S2C, [Save to disk]
  • Re-refined 1l2b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1L2B 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 1L2B
  • 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 1L2B, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l2ba1, region A:135-223 [Jmol] [rasmolscript] [script source]
        - Domain d1l2ba2, region A:2-134 [Jmol] [rasmolscript] [script source]
        - Domain d1l2ba3, region A:233-274 [Jmol] [rasmolscript] [script source]
  • 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: [1l2b_D] [1l2b] [1l2b_B] [1l2b_A] [1l2b_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1L2B: [Fapy_DNA_glyco] [H2TH ] by SMART
    • Other resources with information on 1L2B
  • Community annotation for 1L2B 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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