3GB9 Transferase date Feb 19, 2009
title Human Purine Nucleoside Phosphorylase Double Mutant E201q,N2 Complexed With 2-Fluoroadenine
authors M.R.Sawaya, S.Afshar
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: A, B, C
Synonym: Pnp, Inosine Phosphorylase
Ec: 2.4.2.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Np, Pnp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.791 130.648 149.177 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand A2F, GOL, SO4 enzyme Transferase E.C.2.4.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine., Afshar S, Sawaya MR, Morrison SL, Protein Sci. 2009 May;18(5):1107-14. PMID:19388075
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (3gb9.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 3GB9
  • CSU: Contacts of Structural Units for 3GB9
  • Likely Quarternary Molecular Structure file(s) for 3GB9
  • Structure Factors (765 Kb)
  • Retrieve 3GB9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GB9 from S2C, [Save to disk]
  • Re-refined 3gb9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GB9 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 3GB9
  • 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 3GB9, from MSDmotif at EBI
  • Fold representative 3gb9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gb9_C] [3gb9] [3gb9_A] [3gb9_B]
  • SWISS-PROT database: [P00491]
  • Domain organization of [PNPH_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3GB9 with the sequences similar proteins can be viewed for 3GB9'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 3GB9
  • Community annotation for 3GB9 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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