4UTX Hydrolase date Jul 23, 2014
title Crystal Structure Of Zebrafish Sirtuin 5 In Complex With 3- Nitro-Propionylated Cps1-Peptide
authors M.Pannek, M.Gertz, C.Steegborn
compound source
Molecule: Nad-Dependent Protein Deacylase Sirtuin-5, Mitoch
Chain: A, B
Fragment: Catalytic Core, Unp Residues 30-298
Synonym: Sirtuin 5, Regulatory Protein Sir2 Homolog 5
Ec: 3.5.1.-
Engineered: Yes
Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus
Expression_system_vector: Pet151

Molecule: Carbamoylphosphate Synthetase I
Chain: C
Fragment: Unp Residues 524-531
Synonym: 3-Nitro-Propionyl-Cps1 Peptide
Other_details: Benzoylated Glycine At Position 1. 3-Nitro- Propionylated Lysine At Position 4

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 65 2 2
R_factor 0.19357 R_Free 0.26189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.490 87.490 313.790 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand 3NP, BEZ, DMS, EDO, EPE, NA, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceChemical Probing of the Human Sirtuin 5 Active Site Reveals Its Substrate Acyl Specificity and Peptide-Based Inhibitors., Roessler C, Nowak T, Pannek M, Gertz M, Nguyen GT, Scharfe M, Born I, Sippl W, Steegborn C, Schutkowski M, Angew Chem Int Ed Engl. 2014 Aug 11. doi: 10.1002/anie.201402679. PMID:25111069
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (178 Kb) [Save to disk]
  • Biological Unit Coordinates (4utx.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (4utx.pdb2.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 4UTX
  • CSU: Contacts of Structural Units for 4UTX
  • Structure Factors (124 Kb)
  • Retrieve 4UTX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UTX from S2C, [Save to disk]
  • Re-refined 4utx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UTX 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 4UTX
  • 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 4UTX, from MSDmotif at EBI
  • Fold representative 4utx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4utx_A] [4utx_B] [4utx] [4utx_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4UTX: [ZnF_C2HC ] by SMART
  • Other resources with information on 4UTX
  • Community annotation for 4UTX at PDBWiki (http://pdbwiki.org)

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