3D1V Transferase date May 06, 2008
title Crystal Structure Of Human Pnp Complexed With 2-Mercapto(3h) Quinazolinone
authors W.F.De Azevedo Jr., L.A.Basso, D.S.Santos
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: A
Synonym: Inosine Phosphorylase, Pnp
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Np, Pnp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: H 3 2
R_factor 0.221 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
138.666 138.666 159.379 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand D1V, SO4 enzyme Transferase E.C. BRENDA

Primary referenceStructural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function., Timmers LF, Caceres RA, Vivan AL, Gava LM, Dias R, Ducati RG, Basso LA, Santos DS, de Azevedo WF Jr, Arch Biochem Biophys. 2008 Nov 1;479(1):28-38. Epub 2008 Aug 30. PMID:18790691
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (3d1v.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 3D1V
  • CSU: Contacts of Structural Units for 3D1V
  • Likely Quarternary Molecular Structure file(s) for 3D1V
  • Structure Factors (259 Kb)
  • Retrieve 3D1V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D1V from S2C, [Save to disk]
  • Re-refined 3d1v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D1V 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 3D1V
  • 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 3D1V, from MSDmotif at EBI
  • Fold representative 3d1v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d1v_A] [3d1v]
  • SWISS-PROT database: [P00491]
  • Domain organization of [PNPH_HUMAN] by SWISSPFAM
  • Other resources with information on 3D1V
  • Community annotation for 3D1V 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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