3N9V Hydrolase date May 31, 2010
title Crystal Structure Of Inpp5b
authors L.Tresaugues, M.Welin, C.H.Arrowsmith, H.Berglund, C.Bountra, R.C A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Jo T.Karlberg, S.Kol, T.Kotenyova, M.Moche, T.Nyman, C.Persson, H.Sc P.Schutz, M.I.Siponen, A.G.Thorsell, S.Van Der Berg, E.Wahlberg J.Weigelt, M.Wisniewska, P.Nordlund, Structural Genomics Conso (Sgc)
compound source
Molecule: Type II Inositol-1,4,5-Trisphosphate 5-Phosphatas
Chain: A, B
Fragment: Unp Residues 342-647
Synonym: Phosphoinositide 5-Phosphatase, 5ptase, 75 Kda Ino Polyphosphate-5-Phosphatase;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Inpp5b
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) R3 Prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Ch2
symmetry Space Group: I 21 21 21
R_factor 0.190 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
96.160 110.660 159.380 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand CA, GOL, MG enzyme Hydrolase E.C. BRENDA
A, B

Primary referenceStructural Basis for Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases., Tresaugues L, Silvander C, Flodin S, Welin M, Nyman T, Graslund S, Hammarstrom M, Berglund H, Nordlund P, Structure. 2014 Apr 2. pii: S0969-2126(14)00073-2. doi:, 10.1016/j.str.2014.01.013. PMID:24704254
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (204 Kb) [Save to disk]
  • Biological Unit Coordinates (3n9v.pdb1.gz) 102 Kb
  • Biological Unit Coordinates (3n9v.pdb2.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 3N9V
  • CSU: Contacts of Structural Units for 3N9V
  • Structure Factors (1334 Kb)
  • Retrieve 3N9V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3N9V from S2C, [Save to disk]
  • Re-refined 3n9v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3N9V 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 3N9V
  • 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 3N9V, from MSDmotif at EBI
  • Fold representative 3n9v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3n9v] [3n9v_B] [3n9v_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3N9V: [IPPc ] by SMART
  • Other resources with information on 3N9V
  • Community annotation for 3N9V 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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