2H4J	Hydrolase	date	May 24, 2006
title	Sir2-Deacetylated Peptide (From Enzymatic Turnover In Crystal)
authors	K.G.Hoff, J.L.Avalos, K.Sens, 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 Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl-21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11a
Molecule: Cellular Tumor Antigen P53 Chain: D Synonym: Tumor Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13; Engineered: Yes		Synthetic: Yes Other_details: F-Moc Synthesized Peptide
symmetry	Space Group: P 21 21 21	R_factor 0.198 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 46.049 59.683 107.350 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	NCA, OAD, 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	Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide., Hoff KG, Avalos JL, Sens K, Wolberger C, Structure. 2006 Aug;14(8):1231-40. PMID:16905097

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk] Biological Unit Coordinates (2h4j.pdb1.gz) 84 Kb LPC: Ligand-Protein Contacts for 2H4J CSU: Contacts of Structural Units for 2H4J Likely Quarternary Molecular Structure file(s) for 2H4J Structure Factors (164 Kb) Retrieve 2H4J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2H4J from S2C, [Save to disk] Re-refined 2h4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2H4J 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 2H4J

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 2H4J, from MSDmotif at EBI Fold representative 2h4j from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2h4j_A] [2h4j_D] SWISS-PROT database: [Q9WYW0] [P04637] Domain organization of [NPD_THEMA] [P53_HUMAN] by SWISSPFAM Alignments of the sequence of 2H4J with the sequences similar proteins can be viewed for 2H4J'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 2H4J

Community annotation for 2H4J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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