3D1V	Transferase	date	May 06, 2008
title	Crystal Structure Of Human Pnp Complexed With 2-Mercapto(3h) Quinazolinone
authors	W.F.De Azevedo Jr., L.A.Basso, D.S.Santos
compound		source
Molecule: Purine Nucleoside Phosphorylase Chain: A Synonym: Inosine Phosphorylase, Pnp Ec: 2.4.2.1 Engineered: 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 0.221 R_Free 0.277
crystal cell	length a length b length c angle alpha angle beta angle gamma 138.666 138.666 159.379 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	D1V, SO4	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	Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function., Timmers LF, Caceres RA, Vivan AL, Gava LM, Dias R, Ducati RG, Basso LA, Santos DS, de Azevedo WF Jr, Arch Biochem Biophys. 2008 Nov 1;479(1):28-38. Epub 2008 Aug 30. PMID:18790691

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk] Biological Unit Coordinates (3d1v.pdb1.gz) 142 Kb LPC: Ligand-Protein Contacts for 3D1V CSU: Contacts of Structural Units for 3D1V Likely Quarternary Molecular Structure file(s) for 3D1V Structure Factors (259 Kb) Retrieve 3D1V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3D1V from S2C, [Save to disk] Re-refined 3d1v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D1V 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 3D1V

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 3D1V, from MSDmotif at EBI Fold representative 3d1v from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d1v_A] SWISS-PROT database: [P00491] Domain organization of [PNPH_HUMAN] by SWISSPFAM Alignments of the sequence of 3D1V with the sequences similar proteins can be viewed for 3D1V'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 3D1V

Community annotation for 3D1V at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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