1KO9 Hydrolase date Dec 20, 2001
title Native Structure Of The Human 8-Oxoguanine Dna Glycosylase Hogg1
authors M.Bjoras, E.Seeberg, L.Luna, L.H.Pearl, T.E.Barrett
compound source
Molecule: 8-Oxoguanine Dna Glycosylase
Chain: A
Synonym: N-Glycosylasedna Lyase
Ec: 3.2.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ogg1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bk3010
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc18
symmetry Space Group: P 65
R_factor 0.206 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.513 105.513 47.597 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.15 Å
ligand SO4 enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 1LWW, 1N3A
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceReciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase., Bjoras M, Seeberg E, Luna L, Pearl LH, Barrett TE, J Mol Biol 2002 Mar 22;317(2):171-7. PMID:11902834
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1ko9.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 1KO9
  • CSU: Contacts of Structural Units for 1KO9
  • Likely Quarternary Molecular Structure file(s) for 1KO9
  • Retrieve 1KO9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KO9 from S2C, [Save to disk]
  • View 1KO9 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 1KO9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KO9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ko9a2, region A:12-135 [Jmol] [rasmolscript] [script source]
        - Domain d1ko9a1, region A:136-323 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ko9 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: [1ko9_A] [1ko9]
  • SWISS-PROT database: [O15527]
  • Domain organization of [OGG1_HUMAN] by SWISSPFAM
  • Domain found in 1KO9: [ENDO3c ] by SMART
  • Other resources with information on 1KO9
  • Community annotation for 1KO9 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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