4UTZ Hydrolase date Jul 24, 2014
title Crystal Structure Of Zebrafish Sirtuin 5 In Complex With Adipoylated Cps1-Peptide
authors M.Pannek, M.Gertz, C.Steegborn
compound source
Molecule: Sirtuin 5
Chain: A, B
Fragment: Catalytic Core, Residues 30-298
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_type: Plasmid
Expression_system_vector: Pet151

Molecule: Carbamoylphosphate Synthetase I
Chain: D
Fragment: Unp Residues 524-531
Synonym: Adipoyl-Cps1 Peptide
Other_details: Benzoylated Glycine At Position 1 Adipoylate At Position 4

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 65 2 2
R_factor 0.20934 R_Free 0.25437
length a length b length c angle alpha angle beta angle gamma
87.320 87.320 314.570 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand 0L1, BEZ, DMS, EDO, EPE, NA, ZN enzyme Hydrolase E.C.3.5.1 BRENDA
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] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (4utz.pdb1.gz) 89 Kb
  • Biological Unit Coordinates (4utz.pdb2.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 4UTZ
  • CSU: Contacts of Structural Units for 4UTZ
  • Structure Factors (104 Kb)
  • Retrieve 4UTZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UTZ from S2C, [Save to disk]
  • Re-refined 4utz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UTZ 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 4UTZ
  • 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 4UTZ, from MSDmotif at EBI
  • Fold representative 4utz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4utz] [4utz_A] [4utz_B] [4utz_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4UTZ: [ZnF_C2HC ] by SMART
  • Other resources with information on 4UTZ
  • Community annotation for 4UTZ at PDBWiki (http://pdbwiki.org)

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