3INY Transferase date Aug 13, 2009
title Crystal Structure Of Human Purine Nucleoside Phosphorylase I With 7-Deazaguanine
authors W.F.De Azevedo Jr, D.S.Santos, L.A.Basso
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: A
Synonym: Pnp, Inosine Phosphorylase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Np, Pnp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3 2
R_factor 0.209 R_Free 0.269
length a length b length c angle alpha angle beta angle gamma
138.748 138.748 159.366 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.75 Å
ligand 7DG, SO4 enzyme Transferase E.C. BRENDA

Primary referenceCrystal structure and molecular dynamics studies of human purine nucleoside phosphorylase complexed with 7-deazaguanine., Caceres RA, Timmers LF, Pauli I, Gava LM, Ducati RG, Basso LA, Santos DS, de Azevedo WF Jr, J Struct Biol. 2010 Mar;169(3):379-88. Epub 2009 Nov 22. PMID:19932753
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (3iny.pdb1.gz) 48 Kb
  • Biological Unit Coordinates (3iny.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 3INY
  • CSU: Contacts of Structural Units for 3INY
  • Structure Factors (246 Kb)
  • Retrieve 3INY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3INY from S2C, [Save to disk]
  • Re-refined 3iny structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3INY 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 3INY
  • 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 3INY, from MSDmotif at EBI
  • Fold representative 3iny from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iny_A] [3iny]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3INY
  • Community annotation for 3INY 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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