3RIG Hydrolase date Apr 13, 2011
title Sirt5 Is An Nad-Dependent Protein Lysine Demalonylase And Desuccinylase
authors Y.Zhou
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 Thioacetyl-Lysine 9
Chain: C, D
Engineered: Yes

Synthetic: Yes
Other_details: This Human Histone 3 N-Terminal Was Chemical Modified On Residue Lysine 9 With Thioacetyl.
symmetry Space Group: P 21 21 21
R_factor 0.219 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
52.538 67.876 156.749 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand NHE, TLY, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
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] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (3rig.pdb1.gz) 89 Kb
  • Biological Unit Coordinates (3rig.pdb2.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 3RIG
  • CSU: Contacts of Structural Units for 3RIG
  • Structure Factors (534 Kb)
  • Retrieve 3RIG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RIG from S2C, [Save to disk]
  • Re-refined 3rig structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RIG 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 3RIG
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3RIG, from MSDmotif at EBI
  • Fold representative 3rig from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rig_D] [3rig_C] [3rig_B] [3rig_A] [3rig]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RIG
  • Community annotation for 3RIG at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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