3BGS Transferase date Nov 27, 2007
title Structure Of Human Purine Nucleoside Phosphorylase With L- Dadme-Immh And Phosphate
authors A.S.Murkin, U.A.Ramagopal, S.C.Almo, V.L.Schramm
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: A
Synonym: Inosine Phosphorylase; Pnp
Ec: 2.4.2.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Bl21(De3)
Gene: Np, Pnp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcr-T7ct-Topo
symmetry Space Group: H 3 2
R_factor 0.218 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
142.801 142.801 167.348 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand DIH, PO4 BindingDB enzyme Transferase E.C.2.4.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceL-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase., Rinaldo-Matthis A, Murkin AS, Ramagopal UA, Clinch K, Mee SP, Evans GB, Tyler PC, Furneaux RH, Almo SC, Schramm VL, J Am Chem Soc. 2008 Jan 23;130(3):842-4. Epub 2007 Dec 23. PMID:18154341
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (3bgs.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 3BGS
  • CSU: Contacts of Structural Units for 3BGS
  • Likely Quarternary Molecular Structure file(s) for 3BGS
  • Structure Factors (269 Kb)
  • Retrieve 3BGS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BGS from S2C, [Save to disk]
  • Re-refined 3bgs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BGS 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 3BGS
  • 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 3BGS, from MSDmotif at EBI
  • Fold representative 3bgs from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bgs] [3bgs_A]
  • SWISS-PROT database: [P00491]
  • Domain organization of [PNPH_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3BGS with the sequences similar proteins can be viewed for 3BGS'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 3BGS
  • Community annotation for 3BGS 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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