3PHB Transferase Transferase Inhibitor date Nov 03, 2010
title Crystal Structure Of Human Purine Nucleoside Phosphorylase I With Dadme-Immg
authors M.Ho, M.B.Cassera, A.S.Murkin, S.C.Almo, V.L.Schramm
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: E, Q, S, T, U, Y
Synonym: Pnp, Inosine Phosphorylase
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pnp, Np
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcr-T7nt-Topo
symmetry Space Group: C 1 2 1
R_factor 0.230 R_Free 0.295
length a length b length c angle alpha angle beta angle gamma
269.270 52.632 128.119 90.00 90.33 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand IM5, PO4 BindingDB enzyme Transferase E.C. BRENDA
S, Q, T, Y, E, U

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (3phb.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (3phb.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 3PHB
  • CSU: Contacts of Structural Units for 3PHB
  • Structure Factors (1256 Kb)
  • Retrieve 3PHB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PHB from S2C, [Save to disk]
  • Re-refined 3phb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PHB 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 3PHB
  • 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 3PHB, from MSDmotif at EBI
  • Fold representative 3phb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3phb_Y] [3phb_U] [3phb] [3phb_Q] [3phb_E] [3phb_T] [3phb_S]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3PHB with the sequences similar proteins can be viewed for 3PHB'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 3PHB
  • Community annotation for 3PHB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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