5TKM Hydrolase date Oct 07, 2016
title Crystal Structure Of Human Apobec3b N-Terminal Domain
authors X.Xiao, H.Yang, V.Arutiunian, G.Besse, C.Morimoto, B.Zirkle, X.S.C
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 K-12
Expression_system_taxid: 83333
symmetry Space Group: P 21 21 21
R_factor 0.188 R_Free 0.203
length a length b length c angle alpha angle beta angle gamma
60.739 60.802 111.515 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ZN enzyme Hydrolase E.C.3.5.4 BRENDA
A, B

Primary referenceStructural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation., Xiao X, Yang H, Arutiunian V, Fang Y, Besse G, Morimoto C, Zirkle B, Chen XS, Nucleic Acids Res. 2017 Jul 7;45(12):7494-7506. doi: 10.1093/nar/gkx362. PMID:28575276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (5tkm.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (5tkm.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 5TKM
  • CSU: Contacts of Structural Units for 5TKM
  • Structure Factors (985 Kb)
  • Retrieve 5TKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TKM from S2C, [Save to disk]
  • Re-refined 5tkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TKM 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 5TKM
  • 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 5tkm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tkm_B] [5tkm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TKM
  • Community annotation for 5TKM at PDBWiki (http://pdbwiki.org)

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