3IR2 Hydrolase date Aug 21, 2009
title Crystal Structure Of The Apobec3g Catalytic Domain
authors S.M.D.Shandilya, C.A.Schiffer
compound source
Molecule: Dna Dc->Du-Editing Enzyme Apobec-3g
Chain: A, B
Fragment: C-Terminal Domain
Synonym: Apobec-Related Cytidine Deaminase, Arcd, Apobec-Re Protein, Arp-9, Cem-15, Cem15;
Ec: 3.5.4.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apobec3g, Mds019
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus De3-(Ril)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p1
symmetry Space Group: P 21 21 21
R_factor 0.166 R_Free 0.208
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.338 72.532 97.433 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand CL, MG, ZN enzyme Hydrolase E.C.3.5.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces., Shandilya SM, Nalam MN, Nalivaika EA, Gross PJ, Valesano JC, Shindo K, Li M, Munson M, Royer WE, Harjes E, Kono T, Matsuo H, Harris RS, Somasundaran M, Schiffer CA, Structure. 2010 Jan 13;18(1):28-38. PMID:20152150
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (3ir2.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (3ir2.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 3IR2
  • CSU: Contacts of Structural Units for 3IR2
  • Structure Factors (173 Kb)
  • Retrieve 3IR2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IR2 from S2C, [Save to disk]
  • Re-refined 3ir2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IR2 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 3IR2
  • 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
  • 3D motif for 3IR2, from MSDmotif at EBI
  • Fold representative 3ir2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ir2_A] [3ir2_B] [3ir2]
  • SWISS-PROT database: [Q9HC16]
  • Domain organization of [ABC3G_HUMAN] by SWISSPFAM
  • Other resources with information on 3IR2
  • Community annotation for 3IR2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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