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 Diffraction	resolution	1.80 Å
ligand	PRK, ZN	enzyme	Hydrolase E.C.3.5.1 BRENDA
Gene	TM
Gene Ontology	Chain Function Process Component A hydrolase activity protein-malonyllysine demalo... protein-succinyllysine desuc... metal ion binding NAD+ binding cytoplasm
Primary reference	Structure 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. 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_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.

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, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---