5P05 Hydrolase date Jun 28, 2016
title Automated Refinement Of Diffraction Data Obtained From An Endothiapepsin Crystal Treated With Fragment 52
authors J.Schiebel, A.Heine, G.Klebe
compound source
Molecule: Endothiapepsin
Chain: A
Ec: 3.4.23.22
Organism_scientific: Cryphonectria Parasitica
Organism_taxid: 5116
symmetry Space Group: P 1 21 1
R_factor 0.158 R_Free 0.197
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.074 72.960 52.495 90.00 109.52 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand
enzyme Hydrolase E.C.3.4.23.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHigh-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits., Schiebel J, Krimmer SG, Rower K, Knorlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glockner S, Weiss MS, Mueller U, Klebe G, Heine A, Structure. 2016 Aug 2;24(8):1398-409. doi: 10.1016/j.str.2016.06.010. Epub 2016, Jul 21. PMID:27452405
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (5p05.pdb1.gz) 141 Kb
  • CSU: Contacts of Structural Units for 5P05
  • Structure Factors (369 Kb)
  • Retrieve 5P05 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5P05 from S2C, [Save to disk]
  • Re-refined 5p05 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5P05 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 5P05
  • 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: [5p05] [5p05_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5P05
  • Community annotation for 5P05 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science