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 Diffraction	resolution	1.40 Å
ligand	ALY, NCA, ZN	enzyme	Hydrolase E.C.3.5.1 BRENDA
Gene Ontology	Chain Function Process Component A hydrolase activity protein-malonyllysine demalo... protein-succinyllysine desuc... metal ion binding NAD+ binding cytoplasm
Primary reference	Mechanism 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_B] SWISS-PROT database: [Q9WYW0] [P04637] 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)

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