4B1I Hydrolase date Jul 10, 2012
title Structure Of Human Parg Catalytic Domain In Complex With Oa-
authors C.Brassington, J.Ellston, G.Hassall, G.Holdgate, T.Johnson, M.Mca G.Smith, J.A.Tucker, M.Watson
compound source
Molecule: Poly(Adp-Ribose) Glycohydrolase
Chain: A
Fragment: Catalytic Domain, Residues 448-976
Synonym: Polyadp-Ribose Glycohydrolase
Ec: 3.2.1.143
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-6his
symmetry Space Group: P 21 21 21
R_factor 0.160 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.687 90.407 94.290 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand A8P, DTV, GOL, SO4 enzyme Hydrolase E.C.3.2.1.143 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of the Human Poly (ADP-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by ADP-HPD Derivatives., Tucker JA, Bennett N, Brassington C, Durant ST, Hassall G, Holdgate G, McAlister M, Nissink JW, Truman C, Watson M, PLoS One. 2012;7(12):e50889. doi: 10.1371/journal.pone.0050889. Epub 2012 Dec 10. PMID:23251397
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (4b1i.pdb1.gz) 176 Kb
  • LPC: Ligand-Protein Contacts for 4B1I
  • CSU: Contacts of Structural Units for 4B1I
  • Structure Factors (443 Kb)
  • Retrieve 4B1I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B1I from S2C, [Save to disk]
  • Re-refined 4b1i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B1I 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 4B1I
  • 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 4B1I, from MSDmotif at EBI
  • Fold representative 4b1i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b1i_A] [4b1i]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4B1I
  • Community annotation for 4B1I at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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