5CQD Hydrolase date Jul 21, 2015
title Crystal Structure Of The Cancer Genomic Dna Mutator Apobec3b
authors K.Shi, K.Kurahashi, H.Aihara
compound source
Molecule: Dna Dc->Du-Editing Enzyme Apobec-3b
Chain: A, C
Fragment: Unp Residues 187-378
Synonym: A3b,Phorbolin-1-Related Protein,Phorbolin-23
Ec: 3.5.4.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apobec3b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.440 50.840 70.150 90.00 100.83 90.00
method X-Ray Diffractionresolution 2.08 Å
ligand GOL, ZN enzyme Hydrolase E.C.3.5.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceCrystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain., Shi K, Carpenter MA, Kurahashi K, Harris RS, Aihara H, J Biol Chem. 2015 Sep 28. pii: jbc.M115.679951. PMID:26416889
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (190 Kb) [Save to disk]
  • Biological Unit Coordinates (5cqd.pdb1.gz) 93 Kb
  • Biological Unit Coordinates (5cqd.pdb2.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 5CQD
  • CSU: Contacts of Structural Units for 5CQD
  • Structure Factors (390 Kb)
  • Retrieve 5CQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CQD from S2C, [Save to disk]
  • Re-refined 5cqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CQD 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 5CQD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cqd_A] [5cqd_C] [5cqd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5CQD
  • Community annotation for 5CQD at PDBWiki (http://pdbwiki.org)

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