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
  • Alignments of the sequence of 3INY with the sequences similar proteins can be viewed for 3INY's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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