3GB9	Transferase	date	Feb 19, 2009
title	Human Purine Nucleoside Phosphorylase Double Mutant E201q,N2 Complexed With 2-Fluoroadenine
authors	M.R.Sawaya, S.Afshar
compound		source
Molecule: Purine Nucleoside Phosphorylase Chain: A, B, C Synonym: Pnp, Inosine Phosphorylase 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_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet16b
symmetry	Space Group: P 21 21 21	R_factor 0.184 R_Free 0.227
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.791 130.648 149.177 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	A2F, GOL, SO4	enzyme	Transferase E.C.2.4.2.1 BRENDA
Gene Ontology	Chain Function Process Component A, C, B 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	Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine., Afshar S, Sawaya MR, Morrison SL, Protein Sci. 2009 May;18(5):1107-14. PMID:19388075

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk] Biological Unit Coordinates (3gb9.pdb1.gz) 140 Kb LPC: Ligand-Protein Contacts for 3GB9 CSU: Contacts of Structural Units for 3GB9 Likely Quarternary Molecular Structure file(s) for 3GB9 Structure Factors (792 Kb) Retrieve 3GB9 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GB9 from S2C, [Save to disk] Re-refined 3gb9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GB9 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 3GB9

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 3GB9, from MSDmotif at EBI Fold representative 3gb9 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gb9_A] [3gb9_B] [3gb9_C] SWISS-PROT database: [P00491] Domain organization of [PNPH_HUMAN] by SWISSPFAM Alignments of the sequence of 3GB9 with the sequences similar proteins can be viewed for 3GB9'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 3GB9

Community annotation for 3GB9 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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