2H59 Hydrolase date May 25, 2006
title Sir2 H116a-Deacetylated P53 Peptide-3'-O-Acetyl Adp Ribose
authors K.G.Hoff, J.L.Avalos, K.Sens, C.Wolberger
compound source
Molecule: Nad-Dependent Deacetylase
Chain: A, B
Synonym: Regulatory Protein Sir2 Homolog
Ec: 3.5.1.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336
Gene: Npda
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet11a

Molecule: Cellular Tumor Antigen P53
Chain: D, E
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13;
Engineered: Yes

Synthetic: Yes
Other_details: Fmoc Synthesized Peptide
symmetry Space Group: P 41
R_factor 0.205 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.996 46.996 257.081 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 3OD, APR, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceInsights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide., Hoff KG, Avalos JL, Sens K, Wolberger C, Structure. 2006 Aug;14(8):1231-40. PMID:16905097
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (2h59.pdb1.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 2H59
  • CSU: Contacts of Structural Units for 2H59
  • Likely Quarternary Molecular Structure file(s) for 2H59
  • Structure Factors (193 Kb)
  • Retrieve 2H59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H59 from S2C, [Save to disk]
  • Re-refined 2h59 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H59 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 2H59
  • 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 2H59, from MSDmotif at EBI
  • Fold representative 2h59 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h59] [2h59_A] [2h59_D] [2h59_E] [2h59_B]
  • SWISS-PROT database: [Q9WYW0] [P04637]
  • Belongs to the pore-forming pnc-27 peptide of 32 aas from the p53 tumor suppressor protein (pnc-27) family according to TCDB.
  • Domain organization of [NPD_THEMA] [P53_HUMAN] by SWISSPFAM
  • Other resources with information on 2H59
  • Community annotation for 2H59 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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