1VK1 Structural Genomics, Unknown Function date Apr 13, 2004
title Conserved Hypothetical Protein From Pyrococcus Furiosus Pfu-
authors A.Shah, Z.J.Liu, W.Tempel, L.Chen, D.Lee, H.Yang, J.Chang, M.Zhao, J J.Rose, P.S.Brereton, M.Izumi, F.E.Jenney Jr., F.L.Poole Ii, C.S F.J.Sugar, M.W.W.Adams, D.C.Richardson, J.S.Richardson, B.C.Wan Southeast Collaboratory For Structural Genomics (Secsg)
compound source
Molecule: Conserved Hypothetical Protein
Chain: A
Engineered: Yes
Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.165 R_Free 0.175
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.148 40.099 65.671 90.00 122.29 90.00
method X-Ray Diffractionresolution 1.20 Å
ligand MLY, NA, PEG, PO4 enzyme
note 1VK1 is a representative structure
Primary reference(NZ)CH...O contacts assist crystallization of a ParB-like nuclease., Shaw N, Cheng C, Tempel W, Chang J, Ng J, Wang XY, Perrett S, Rose J, Rao Z, Wang BC, Liu ZJ, BMC Struct Biol. 2007 Jul 7;7:46. PMID:17617922
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (1vk1.pdb1.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 1VK1
  • CSU: Contacts of Structural Units for 1VK1
  • Likely Quarternary Molecular Structure file(s) for 1VK1
  • Structure Factors (1540 Kb)
  • Retrieve 1VK1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VK1 from S2C, [Save to disk]
  • Re-refined 1vk1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VK1 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 1VK1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1VK1 from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VK1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vk1a_, region A [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vk1_A] [1vk1]
  • SWISS-PROT database: [Q8U3S5]
  • Domain organization of [Q8U3S5_PYRFU] by SWISSPFAM
  • Domain found in 1VK1: [ParB ] by SMART
  • Other resources with information on 1VK1
  • Community annotation for 1VK1 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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