5JVI Hydrolase date May 11, 2016
title Thermolysin In Complex With Jc148.
authors S.G.Krimmer, J.Cramer, A.Heine, G.Klebe
compound source
Molecule: Thermolysin
Chain: E
Synonym: Thermostable Neutral Proteinase
Ec: 3.4.24.27
 Organism_scientific: Bacillus Thermoproteolyticus
Organism_taxid: 1427
symmetry Space Group: P 61 2 2
R_factor 0.102 R_Free 0.119
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.580 92.580 131.230 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.12 Å
ligand 6QC, CA, DMS, GOL, ZN enzyme Hydrolase E.C.3.4.24.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
E


Primary referenceRational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands., Krimmer SG, Cramer J, Betz M, Fridh V, Karlsson R, Heine A, Klebe G, J Med Chem. 2016 Dec 8;59(23):10530-10548. Epub 2016 Nov 30. PMID:27933956
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (167 Kb) [Save to disk]
  • Biological Unit Coordinates (5jvi.pdb1.gz) 161 Kb
  • LPC: Ligand-Protein Contacts for 5JVI
  • CSU: Contacts of Structural Units for 5JVI
  • Structure Factors (1132 Kb)
  • Retrieve 5JVI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JVI from S2C, [Save to disk]
  • Re-refined 5jvi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JVI 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 5JVI
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jvi_E] [5jvi]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5JVI
  • Community annotation for 5JVI at PDBWiki (http://pdbwiki.org)

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