3PHB	Transferase Transferase Inhibitor	date	Nov 03, 2010
title	Crystal Structure Of Human Purine Nucleoside Phosphorylase I With Dadme-Immg
authors	M.Ho, M.B.Cassera, A.S.Murkin, S.C.Almo, V.L.Schramm
compound		source
Molecule: Purine Nucleoside Phosphorylase Chain: E, Q, S, T, U, Y Synonym: Pnp, Inosine Phosphorylase Ec: 2.4.2.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pnp, Np Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcr-T7nt-Topo
symmetry	Space Group: C 1 2 1	R_factor 0.230 R_Free 0.295
crystal cell	length a length b length c angle alpha angle beta angle gamma 269.270 52.632 128.119 90.00 90.33 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	IM5, PO4 BindingDB	enzyme	Transferase E.C.2.4.2.1 BRENDA
Gene Ontology	Chain Function Process Component S, Q, T, Y, E, U 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

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk] Biological Unit Coordinates (3phb.pdb1.gz) 140 Kb Biological Unit Coordinates (3phb.pdb2.gz) 140 Kb LPC: Ligand-Protein Contacts for 3PHB CSU: Contacts of Structural Units for 3PHB Structure Factors (1289 Kb) Retrieve 3PHB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3PHB from S2C, [Save to disk] Re-refined 3phb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3PHB 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 3PHB

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3phb_E] [3phb_Q] [3phb_S] [3phb_T] [3phb_U] [3phb_Y] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3PHB with the sequences similar proteins can be viewed for 3PHB's classification 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 at ProtoMap. Click on the Cluster number.

Other resources with information on 3PHB

Community annotation for 3PHB at PDBWiki (http://pdbwiki.org)

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