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 Diffraction	resolution	2.59 Å
ligand	IMH, PO4 BindingDB	enzyme	Transferase E.C.2.4.2.1 BRENDA
Gene Ontology	Chain Function Process Component A nucleoside binding purine nucleobase binding purine-nucleoside phosphoryl... drug binding transferase activity transferase activity, transf... phosphate ion binding nucleobase-containing compou... purine nucleobase metabolic ... inosine catabolic process purine nucleotide catabolic ... nicotinamide riboside catabo... immune response NAD biosynthesis via nicotin... urate biosynthetic process positive regulation of T cel... response to drug purine-containing compound s... small molecule metabolic pro... positive regulation of alpha... nucleobase-containing small ... interleukin-2 secretion intracellular cytoplasm cytosol cytoskeleton
Primary reference	Neighboring 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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

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)

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