1YC5 Hydrolase date Dec 21, 2004
title Sir2-P53 Peptide-Nicotinamide
authors J.L.Avalos, M.K.Bever, C.Wolberger
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
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 Ny-Co-13;
Engineered: Yes

Synthetic: Yes
Other_details: The Sequence Of The Peptide Is Naturally Found In Homo Sapiens (Human).
symmetry Space Group: P 21 21 21
R_factor 0.185 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.100 59.749 106.121 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand ALY, NCA, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme., Avalos JL, Bever KM, Wolberger C, Mol Cell 2005 Mar 18;17(6):855-68. PMID:15780941
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1yc5.pdb1.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 1YC5
  • CSU: Contacts of Structural Units for 1YC5
  • Likely Quarternary Molecular Structure file(s) for 1YC5
  • Structure Factors (497 Kb)
  • Retrieve 1YC5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YC5 from S2C, [Save to disk]
  • Re-refined 1yc5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YC5 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 1YC5
  • 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 1YC5, from MSDmotif at EBI
  • Fold representative 1yc5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yc5_A] [1yc5] [1yc5_B]
  • 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
  • Alignments of the sequence of 1YC5 with the sequences similar proteins can be viewed for 1YC5's classification [NPD_THEMA] [P53_HUMAN] 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 [NPD_THEMA] [P53_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YC5
  • Community annotation for 1YC5 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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