3BU0 Oxidoreductase Dna date Dec 31, 2007
title Crystal Structure Of Human Abh2 Cross-Linked To Dsdna With C
authors C.G.Yang, C.Yi, C.He
compound source
Molecule: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb Ho
Chain: A
Synonym: Alkylated Dna Repair Protein Alkb Homolog 2, Oxy D
Ec: 1.14.11.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: 12q24.11
Gene: Alkbh2, Abh2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Dna (5'-D(Cptpgptpaptp(2yr)Paptptpgpc
Chain: B
Engineered: Yes

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 65 2 2
R_factor 0.230 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.591 77.591 227.051 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand 2YR, AKG, MN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA., Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C, Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (3bu0.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 3BU0
  • CSU: Contacts of Structural Units for 3BU0
  • Likely Quarternary Molecular Structure file(s) for 3BU0
  • Structure Factors (116 Kb)
  • Retrieve 3BU0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BU0 from S2C, [Save to disk]
  • Re-refined 3bu0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BU0 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 3BU0
  • 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 3BU0, from MSDmotif at EBI
  • Fold representative 3bu0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bu0] [3bu0_B] [3bu0_C] [3bu0_A]
  • SWISS-PROT database: [Q6NS38]
  • Domain organization of [ALKB2_HUMAN] by SWISSPFAM
  • Other resources with information on 3BU0
  • Community annotation for 3BU0 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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