2OC9 Transferase date Dec 20, 2006
title Crystal Stucture Of Human Purine Nucleoside Phosphorylase Mu With Imm-H
authors A.Rinaldo-Matthis, S.C.Almo, V.L.Schramm
compound source
Molecule: Purine Nucleoside Phosphorylase
Chain: A
Fragment: Purine Nucleoside Phosphorylase
Synonym: Inosine Phosphorylase; Pnp
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_vector_type: Plasmid
symmetry Space Group: H 3 2
R_factor 0.194 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
142.170 142.170 168.674 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.59 Å
ligand IMH, PO4 BindingDB enzyme Transferase E.C.2.4.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNeighboring Group Participation in the Transition State of Human Purine Nucleoside Phosphorylase., Murkin AS, Birck MR, Rinaldo-Matthis A, Shi W, Taylor EA Steven C Almo, Schramm VL, Biochemistry. 2007 May 1;46(17):5038-5049. Epub 2007 Apr 4. PMID:17407325
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (2oc9.pdb1.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 2OC9
  • CSU: Contacts of Structural Units for 2OC9
  • Likely Quarternary Molecular Structure file(s) for 2OC9
  • Structure Factors (167 Kb)
  • Retrieve 2OC9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OC9 from S2C, [Save to disk]
  • Re-refined 2oc9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OC9 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 2OC9
  • 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 2OC9, from MSDmotif at EBI
  • Fold representative 2oc9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oc9]
  • SWISS-PROT database: [P00491]
  • Domain organization of [PNPH_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2OC9 with the sequences similar proteins can be viewed for 2OC9'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 2OC9
  • Community annotation for 2OC9 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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