1YRY	Transferase	date	Feb 05, 2005
title	Crystal Structure Of Human Pnp Complexed With Mesg
authors	R.G.Silva, J.H.Pereira, F.Canduri, L.A.Basso, W.F.De Azevedo Jr. D.S.Santos
compound		source
Molecule: Purine Nucleoside Phosphorylase Chain: E Synonym: Inosine Phosphorylase, Pnp Ec: 2.4.2.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
symmetry	Space Group: H 3 2	R_factor 0.207 R_Free 0.290
crystal cell	length a length b length c angle alpha angle beta angle gamma 138.990 138.990 159.850 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	MSG, SO4	enzyme	Transferase E.C.2.4.2.1 BRENDA
Gene Ontology	Chain Function Process Component E 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	Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thio-guanosine., Silva RG, Pereira JH, Canduri F, de Azevedo WF Jr, Basso LA, Santos DS, Arch Biochem Biophys. 2005 Oct 1;442(1):49-58. PMID:16154528

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk] Biological Unit Coordinates (1yry.pdb1.gz) 50 Kb Biological Unit Coordinates (1yry.pdb2.gz) 146 Kb LPC: Ligand-Protein Contacts for 1YRY CSU: Contacts of Structural Units for 1YRY Likely Quarternary Molecular Structure file(s) for 1YRY Structure Factors (113 Kb) Retrieve 1YRY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YRY from S2C, [Save to disk] Re-refined 1yry structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YRY 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 1YRY

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 1YRY, from MSDmotif at EBI Fold representative 1yry from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1yry_E] SWISS-PROT database: [P00491] Domain organization of [PNPH_HUMAN] by SWISSPFAM Alignments of the sequence of 1YRY with the sequences similar proteins can be viewed for 1YRY'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 1YRY

Community annotation for 1YRY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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