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
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • 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
  • Alignments of the sequence of 3PDH with the sequences similar proteins can be viewed for 3PDH's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3PDH
  • Community annotation for 3PDH 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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