1V3Q Transferase date Nov 04, 2003
title Structure Of Human Pnp Complexed With Ddi
authors F.Canduri, J.H.Pereira, D.M.Dos Santos, R.G.Silva, M.S.Palma, L.A 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
Gene: Pnp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: H 3 2
R_factor 0.214 R_Free 0.306
crystal
cell
length a length b length c angle alpha angle beta angle gamma
141.330 141.330 161.450 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand 2DI, SO4 enzyme Transferase E.C.2.4.2.1 BRENDA
related structures by homologous chain: 1PWY, 1RCT
Gene
Ontology
ChainFunctionProcessComponent
E


Primary referenceStructures of human purine nucleoside phosphorylase complexed with inosine and ddI., Canduri F, dos Santos DM, Silva RG, Mendes MA, Basso LA, Palma MS, de Azevedo WF, Santos DS, Biochem Biophys Res Commun 2004 Jan 23;313(4):907-14. PMID:14706628
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (1v3q.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 1V3Q
  • CSU: Contacts of Structural Units for 1V3Q
  • Likely Quarternary Molecular Structure file(s) for 1V3Q
  • Structure Factors (94 Kb)
  • Retrieve 1V3Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V3Q from S2C, [Save to disk]
  • Re-refined 1v3q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V3Q 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.
  • Visual 3D analysis of 1V3Q
  • 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 1V3Q, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v3qe_, region E [Jmol] [rasmolscript] [script source]
  • Fold representative 1v3q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1v3q] [1v3q_E]
  • SWISS-PROT database: [P00491]
  • Domain organization of [PNPH_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1V3Q with the sequences similar proteins can be viewed for 1V3Q'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 1V3Q
  • Community annotation for 1V3Q at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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