5CQI 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
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 21 21 21
R_factor 0.160 R_Free 0.198
length a length b length c angle alpha angle beta angle gamma
51.020 54.290 65.410 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.68 Å
ligand GOL, ZN enzyme Hydrolase E.C.3.5.4 BRENDA

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] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (5cqi.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 5CQI
  • CSU: Contacts of Structural Units for 5CQI
  • Structure Factors (378 Kb)
  • Retrieve 5CQI in mmCIF format [Save to disk]
  • Re-refined 5cqi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CQI 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 5CQI
  • 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
  • Fold representative 5cqi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cqi_A] [5cqi]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5CQI
  • Community annotation for 5CQI at PDBWiki (http://pdbwiki.org)

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