2DSB Hydrolase date Jun 28, 2006
title Crystal Structure Of Human Adp-Ribose Pyrophosphatase Nudt5
authors M.Zha, C.Zhong, J.Ding
compound source
Molecule: Adp-Sugar Pyrophosphatase
Chain: A, B, C, D
Synonym: Nucleoside Diphosphate-Linked Moiety X Motif 5, Nu 5, Ysa1h;
Ec: 3.6.1.13, 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nudt5
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b(+)
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.717 70.316 87.629 90.00 100.41 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand
enzyme Hydrolase E.C.3.6.1.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate Specificity., Zha M, Zhong C, Peng Y, Hu H, Ding J, J Mol Biol. 2006 Oct 3;. PMID:17052728
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (2dsb.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (2dsb.pdb2.gz) 68 Kb
  • CSU: Contacts of Structural Units for 2DSB
  • Likely Quarternary Molecular Structure file(s) for 2DSB
  • Structure Factors (260 Kb)
  • Retrieve 2DSB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DSB from S2C, [Save to disk]
  • Re-refined 2dsb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DSB 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 2DSB
  • 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
  • 3D motif for 2DSB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dsb_B] [2dsb_C] [2dsb] [2dsb_D] [2dsb_A]
  • SWISS-PROT database: [Q9UKK9]
  • Domain organization of [NUDT5_HUMAN] by SWISSPFAM
  • Other resources with information on 2DSB
  • Community annotation for 2DSB 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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