1QVJ Hydrolase date Aug 27, 2003
title Structure Of Nudt9 Complexed With Ribose-5-Phosphate
authors B.W.Shen, A.L.Perraud, A.S.Scharenberg, B.L.Stoddard
compound source
Molecule: Adp-Ribose Pyrophosphatase
Chain: A
Synonym: Adp-Ribose Diphosphatase, Adenosine Diphosphoribos Pyrophosphatase, Adpr-Ppase, Adp-Ribose Phosphohydrolase, N Diphosphate-Linked Moiety X Motif 9;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nudt9
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Irl+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: I 2 2 2
R_factor 0.212 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
78.900 87.455 120.308 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.91 Å
ligand MG, MSE, RP5, SO4, TRS enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1Q33

Primary referenceThe crystal structure and mutational analysis of human NUDT9., Shen BW, Perraud AL, Scharenberg A, Stoddard BL, J Mol Biol 2003 Sep 12;332(2):385-98. PMID:12948489
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (1qvj.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 1QVJ
  • CSU: Contacts of Structural Units for 1QVJ
  • Likely Quarternary Molecular Structure file(s) for 1QVJ
  • Structure Factors (457 Kb)
  • Retrieve 1QVJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QVJ from S2C, [Save to disk]
  • Re-refined 1qvj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1QVJ 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 1QVJ
  • 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 1QVJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qvja_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1qvj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1qvj] [1qvj_A]
  • SWISS-PROT database: [Q9BW91]
  • Domain organization of [NUDT9_HUMAN] by SWISSPFAM
  • Other resources with information on 1QVJ
  • Community annotation for 1QVJ 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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