3V4K Hydrolase date Dec 15, 2011
title First-In-Class Small Molecule Inhibitors Of The Single-Stran Cytosine Deaminase Apobec3g
authors S.M.D.Shandilya, A.Ali, 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, Apobec-Related Arcd, Apobec-Related Protein 9, 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: 469008
Expression_system_strain: Bl21(De3) Codonplus (Ril)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p1
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.190 72.170 96.810 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.38 Å
ligand CL, MG, ZN enzyme Hydrolase E.C.3.5.4 BRENDA
note 3V4K is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceFirst-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G., Li M, Shandilya SM, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS, ACS Chem Biol. 2012 Jan 17. PMID:22181350
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (3v4k.pdb1.gz) 131 Kb
  • Biological Unit Coordinates (3v4k.pdb2.gz) 131 Kb
  • Biological Unit Coordinates (3v4k.pdb3.gz) 260 Kb
  • Biological Unit Coordinates (3v4k.pdb4.gz) 260 Kb
  • LPC: Ligand-Protein Contacts for 3V4K
  • CSU: Contacts of Structural Units for 3V4K
  • Structure Factors (1231 Kb)
  • Retrieve 3V4K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V4K from S2C, [Save to disk]
  • Re-refined 3v4k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V4K 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 3V4K
  • 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
  • 3D motif for 3V4K, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v4k] [3v4k_A] [3v4k_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3V4K
  • Community annotation for 3V4K at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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