3RIY Hydrolase date Apr 14, 2011
title Sirt5 Is An Nad-Dependent Protein Lysine Demalonylase And Desuccinylase
authors Y.Zhou, Q.Hao
compound source
Molecule: Nad-Dependent Deacetylase Sirtuin-5
Chain: A, B
Fragment: Unp Residues 34-302
Synonym: Sir2-Like Protein 5
Ec: 3.5.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sir2l5, Sirt5
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 R2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdest-F1

Molecule: Peptide Of Histone 3 N-Succinyl Lysine 9
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: Histone 3 (Residue 4-15) Was Chemically Synt
symmetry Space Group: P 21 21 21
R_factor 0.144 R_Free 0.191
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.691 69.417 156.321 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand NAD, SLL, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase., Du J, Zhou Y, Su X, Yu JJ, Khan S, Jiang H, Kim J, Woo J, Kim JH, Choi BH, He B, Chen W, Zhang S, Cerione RA, Auwerx J, Hao Q, Lin H, Science. 2011 Nov 11;334(6057):806-9. PMID:22076378
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (213 Kb) [Save to disk]
  • Biological Unit Coordinates (3riy.pdb1.gz) 105 Kb
  • Biological Unit Coordinates (3riy.pdb2.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 3RIY
  • CSU: Contacts of Structural Units for 3RIY
  • Structure Factors (1097 Kb)
  • Retrieve 3RIY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RIY from S2C, [Save to disk]
  • Re-refined 3riy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RIY 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 3RIY
  • 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 3RIY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3riy_A] [3riy_C] [3riy_B] [3riy] [3riy_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RIY
  • Community annotation for 3RIY at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science