3RZL Oxidoreductase Dna date May 11, 2011
title Duplex Interrogation By A Direct Dna Repair Protein In The S Damage
authors C.Yi, B.Chen, B.Qi, W.Zhang, G.Jia, L.Zhang, C.Li, A.Dinner, C.Yang,
compound source
Molecule: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb Ho
Chain: A, D
Fragment: Unp Residues 56-261
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
Gene: Alkbh2, Abh2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Aptpgptpaptpcpapcptpgpcpg)-3'
Chain: B, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tpcpgpcpapgptpipaptpapcpa)-3'
Chain: C, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.289
length a length b length c angle alpha angle beta angle gamma
55.934 65.006 167.896 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand XL3 enzyme Oxidoreductase E.C.1.14.11 BRENDA
A, D

Primary referenceDuplex interrogation by a direct DNA repair protein in search of base damage., Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C, Nat Struct Mol Biol. 2012 Jun 3;19(7):671-6. doi: 10.1038/nsmb.2320. PMID:22659876
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (3rzl.pdb1.gz) 90 Kb
  • Biological Unit Coordinates (3rzl.pdb2.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 3RZL
  • CSU: Contacts of Structural Units for 3RZL
  • Structure Factors (285 Kb)
  • Retrieve 3RZL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RZL from S2C, [Save to disk]
  • Re-refined 3rzl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RZL 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 3RZL
  • 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 3RZL, from MSDmotif at EBI
  • Fold representative 3rzl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rzl_D] [3rzl_B] [3rzl_C] [3rzl] [3rzl_F] [3rzl_A] [3rzl_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RZL
  • Community annotation for 3RZL at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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