1VLP Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.20962
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.75
ligand CL, EDO, MES, MSE, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • chromatin silencing at telom...

  • Primary referenceThe structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases., Chappie JS, Canaves JM, Han GW, Rife CL, Xu Q, Stevens RC, Structure. 2005 Sep;13(9):1385-96. PMID:16154095
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (298 Kb) [Save to disk]
  • Biological Unit Coordinates (1vlp.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (1vlp.pdb2.gz) 75 Kb
  • Biological Unit Coordinates (1vlp.pdb3.gz) 76 Kb
  • Biological Unit Coordinates (1vlp.pdb4.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 1VLP
  • CSU: Contacts of Structural Units for 1VLP
  • Likely Quarternary Molecular Structure file(s) for 1VLP
  • Structure Factors (15667 Kb)
  • Retrieve 1VLP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VLP from S2C, [Save to disk]
  • Re-refined 1vlp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VLP 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 1VLP
  • 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
  • 3D motif for 1VLP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vlpa1, region A:1-149 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpa2, region A:150-415 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpb1, region B:1-149 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpb2, region B:150-415 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpc1, region C:1-149 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpc2, region C:150-415 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpd1, region D:1-149 [Jmol] [rasmolscript] [script source]
        - Domain d1vlpd2, region D:150-415 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vlp_C] [1vlp] [1vlp_D] [1vlp_A] [1vlp_B]
  • SWISS-PROT database: [P39683]
  • Domain organization of [NPT1_YEAST] by SWISSPFAM
  • Other resources with information on 1VLP
  • Community annotation for 1VLP 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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