3K8O Transferase date Oct 14, 2009
title Crystal Structure Of Human Purine Nucleoside Phosphorylase I With Datme-Immh
authors M.Ho, A.Rinaldo-Matthis, 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: Np, Pnp
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: C 1 2 1
R_factor 0.223 R_Free 0.272
length a length b length c angle alpha angle beta angle gamma
269.212 51.875 129.069 90.00 90.44 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 229, SO4 BindingDB enzyme Transferase E.C. BRENDA
S, Q, T, Y, E, U

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (279 Kb) [Save to disk]
  • Biological Unit Coordinates (3k8o.pdb1.gz) 138 Kb
  • Biological Unit Coordinates (3k8o.pdb2.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 3K8O
  • CSU: Contacts of Structural Units for 3K8O
  • Structure Factors (1081 Kb)
  • Retrieve 3K8O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K8O from S2C, [Save to disk]
  • Re-refined 3k8o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K8O 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 3K8O
  • 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 3K8O, from MSDmotif at EBI
  • Fold representative 3k8o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k8o_U] [3k8o_T] [3k8o_S] [3k8o] [3k8o_E] [3k8o_Y] [3k8o_Q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3K8O
  • Community annotation for 3K8O 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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