1EBM Lyase Dna date Jan 24, 2000
title Crystal Structure Of The Human 8-Oxoguanine Glycosylase (Hogg1) Bound To A Substrate Oligonucleotide
authors S.D.Bruner, D.P.Norman, G.L.Verdine
compound source
Molecule: Dna (5'-D(Gpcpgptpcpcpap(8og) Pgptpcptpapcpc)-3');
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Gpgptpapgpapcpcptpgpgpapcpgpc)-3');
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: 8-Oxoguanine Dna Glycosylase
Chain: A
Fragment: Core Fragment (Residues 12 To 325)
Synonym: Ap Lyase
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30a-Hogg1
symmetry Space Group: P 65 2 2
R_factor 0.232 R_Free 0.263
length a length b length c angle alpha angle beta angle gamma
92.357 92.357 212.872 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand 8OG, CA enzyme
related structures by homologous chain: 1LWW, 1M3H

Primary referenceStructural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA., Bruner SD, Norman DP, Verdine GL, Nature 2000 Feb 24;403(6772):859-66. PMID:10706276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (1ebm.pdb1.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 1EBM
  • CSU: Contacts of Structural Units for 1EBM
  • Likely Quarternary Molecular Structure file(s) for 1EBM
  • Structure Factors (417 Kb)
  • Retrieve 1EBM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EBM from S2C, [Save to disk]
  • Re-refined 1ebm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1EBM 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 1EBM
  • 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 1EBM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ebma1, region A:136-325 [Jmol] [rasmolscript] [script source]
        - Domain d1ebma2, region A:9-135 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ebm 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: [1ebm] [1ebm_D] [1ebm_A] [1ebm_C]
  • SWISS-PROT database: [O15527]
  • Domain organization of [OGG1_HUMAN] by SWISSPFAM
  • Domain found in 1EBM: [ENDO3c ] by SMART
  • Other resources with information on 1EBM
  • Community annotation for 1EBM 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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