5SXG Hydrolase date Aug 09, 2016
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, B
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 0.177 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.390 50.800 76.890 90.00 102.86 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand
enzyme Hydrolase E.C.3.5.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceConformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B., Shi K, Demir O, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H, Sci Rep. 2017 Dec 12;7(1):17415. doi: 10.1038/s41598-017-17694-3. PMID:29234087
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (5sxg.pdb1.gz) 90 Kb
  • Biological Unit Coordinates (5sxg.pdb2.gz) 92 Kb
  • CSU: Contacts of Structural Units for 5SXG
  • Structure Factors (552 Kb)
  • Retrieve 5SXG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5SXG from S2C, [Save to disk]
  • View 5SXG 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 5SXG
  • 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
  • Fold representative 5sxg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5sxg_B] [5sxg_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5SXG
  • Community annotation for 5SXG at PDBWiki (http://pdbwiki.org)

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