2H2D Hydrolase date May 18, 2006
title The Structural Basis For Sirtuin Substrate Affinity
authors M.S.Cosgrove, C.Wolberger
compound source
Molecule: Nad-Dependent Deacetylase
Chain: A
Fragment: Sir2tm
Synonym: Regulatory Protein Sir2 Homolog
Ec: 3.5.1.-
Engineered: Yes
Organism_scientific: Thermotoga Maritima
Organism_taxid: 2336
Gene: Npda
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a

Molecule: Cellular Tumor Antigen P53 Peptide
Chain: B
Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen
Engineered: Yes

Synthetic: Yes
Other_details: The Sequence Of The Peptide Is Naturally Fou Homo Sapiens (Human).
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
45.222 58.698 104.463 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand ALY, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
  • NAD-dependent protein deacet...

  • Primary referenceThe structural basis of sirtuin substrate affinity., Cosgrove MS, Bever K, Avalos JL, Muhammad S, Zhang X, Wolberger C, Biochemistry. 2006 Jun 20;45(24):7511-21. PMID:16768447
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (2h2d.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 2H2D
  • CSU: Contacts of Structural Units for 2H2D
  • Likely Quarternary Molecular Structure file(s) for 2H2D
  • Structure Factors (277 Kb)
  • Retrieve 2H2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H2D from S2C, [Save to disk]
  • Re-refined 2h2d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H2D 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 2H2D
  • 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 2H2D, from MSDmotif at EBI
  • Fold representative 2h2d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h2d_B] [2h2d] [2h2d_A]
  • 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 2H2D
  • Community annotation for 2H2D 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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