3S5A	Oxidoreductase Dna	date	May 21, 2011
title	Abh2 Cross-Linked To Undamaged Dsdna-2 With Cofactors
authors	C.Yi, B.Chen, B.Qi, B.Ramirez, W.Zhang, G.Jia, L.Zhang, C.Q.Li, A.R. C.G.Yang, C.He
compound		source
Molecule: Alpha-Ketoglutarate-Dependent Dioxygenase Alkb Ho Chain: A Fragment: Dioxygenase Domain (Unp Residues 56-258) 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: Abh2, Alkbh2 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: 5'-D(Cptpgptpcptpcpapcptpgptpcpg)-3 Chain: B Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Tpcpgpapcpapgptpgpapgpapcpa)-3 Chain: C Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.197 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 45.968 60.610 65.588 90.00 90.52 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	AKG, GOL, MN, XL3	enzyme	Oxidoreductase E.C.1.14.11 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Duplex 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] (109 Kb) [Save to disk] Biological Unit Coordinates (3s5a.pdb1.gz) 104 Kb LPC: Ligand-Protein Contacts for 3S5A CSU: Contacts of Structural Units for 3S5A Structure Factors (347 Kb) Retrieve 3S5A in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3S5A from S2C, [Save to disk] Re-refined 3s5a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3S5A 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 3S5A

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 3D motif for 3S5A, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3s5a_C] [3s5a_B] [3s5a] [3s5a_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3S5A

Community annotation for 3S5A at PDBWiki (http://pdbwiki.org)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---