3PDH Hydrolase date Oct 22, 2010
title Structure Of Sir2tm Bound To A Propionylated Peptide
authors C.Wolberger, P.Bheda
compound source
Molecule: Nad-Dependent Deacetylase
Chain: A
Synonym: Regulatory Protein Sir2 Homolog
Ec: 3.5.1.-
Engineered: Yes
Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336
Gene: Npda, Sir2, Tm_0490
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: T7 Based Inducible Vector
Expression_system_plasmid: Pet11a

Molecule: Cellular Tumor Antigen P53 18-Residue Peptide
Chain: D
Synonym: Antigen Ny-Co-13, Phosphoprotein P53, Tumor Suppre
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Propionylated P53 Pep
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.561 60.013 106.345 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand PRK, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
Gene TM
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of Sir2Tm bound to a propionylated peptide., Bheda P, Wang JT, Escalante-Semerena JC, Wolberger C, Protein Sci. 2011 Jan;20(1):131-9. PMID:21080423
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (3pdh.pdb1.gz) 94 Kb
  • LPC: Ligand-Protein Contacts for 3PDH
  • CSU: Contacts of Structural Units for 3PDH
  • Structure Factors (207 Kb)
  • Retrieve 3PDH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PDH from S2C, [Save to disk]
  • Re-refined 3pdh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PDH in 3D
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  • Visual 3D analysis of 3PDH
  • 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 3PDH, from MSDmotif at EBI
  • Fold representative 3pdh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pdh] [3pdh_A] [3pdh_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3PDH
  • Community annotation for 3PDH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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