1EBM

CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE

Structural Biology Knowledgebase: 1EBM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.232

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1EBM

Classification: LYASE / DNA

Total Structure Weight: 44884.67


Macromolecule Entities
Molecule Chains Length Organism Details
8-OXOGUANINE DNA GLYCOSYLASE A 317 Homo sapiens Fragment: CORE FRAGMENT (RESIDUES 12 TO 325)
Mutation: R9G, R10S, M11E, K249Q
Gene Name(s): OGG1 Gene View MMH MUTM OGH1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3') C 15 synthetic
DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3') D 15 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
C DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.232
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.36 α = 90.00
b = 92.36 β = 90.00
c = 212.87 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-24
  • Released Date: 2000-03-20
  • Deposition author(s): Bruner, S.D., Norman, D.P., Verdine, G.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4