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

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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