1YRY Transferase date Feb 05, 2005
title Crystal Structure Of Human Pnp Complexed With Mesg
authors R.G.Silva, J.H.Pereira, F.Canduri, L.A.Basso, W.F.De Azevedo Jr. D.S.Santos
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: E
Synonym: Inosine Phosphorylase, Pnp
Ec: 2.4.2.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: H 3 2
R_factor 0.207 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.990 138.990 159.850 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand MSG, SO4 enzyme Transferase E.C.2.4.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
E


Primary referenceKinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine., Silva RG, Pereira JH, Canduri F, de Azevedo WF Jr, Basso LA, Santos DS, Arch Biochem Biophys. 2005 Oct 1;442(1):49-58. PMID:16154528
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1yry.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (1yry.pdb2.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 1YRY
  • CSU: Contacts of Structural Units for 1YRY
  • Likely Quarternary Molecular Structure file(s) for 1YRY
  • Structure Factors (113 Kb)
  • Retrieve 1YRY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YRY from S2C, [Save to disk]
  • Re-refined 1yry structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YRY 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 1YRY
  • 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 1YRY, from MSDmotif at EBI
  • Fold representative 1yry from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yry_E] [1yry]
  • SWISS-PROT database: [P00491]
  • Domain organization of [PNPH_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1YRY with the sequences similar proteins can be viewed for 1YRY's classification [PNPH_HUMAN] 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 [PNPH_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YRY
  • Community annotation for 1YRY 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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