3VIV Hydrolase Protein Binding date Oct 12, 2011
title 1510-N Membrane-Bound Stomatin-Specific Protease K138a Mutan Complex With A Substrate Peptide
authors H.Yokoyama, I.Matsui, S.Fujii
compound source
Molecule: 441aa Long Hypothetical Nfed Protein
Chain: A, B
Fragment: Residues 16-236
Synonym: 1510-N Membrane Protease
Engineered: Yes
Mutation: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 70601
Strain: Ot3
Gene: Ph1510
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: Ph Stomatin Ph1511
Chain: C
Fragment: Residues 234-243
Synonym: Uncharacterized Protein Ph1511
Engineered: Yes

Synthetic: Yes
Organism_scientific: Pyrococcus Horikoshii Ot3
Organism_taxid: 70601
Other_details: Synthetic Peptide
symmetry Space Group: P 43 21 2
R_factor 0.212 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.473 111.473 91.768 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand CL, GOL, IMD enzyme
Primary referenceCrystal structure of a membrane stomatin-specific protease in complex with a substrate Peptide., Yokoyama H, Takizawa N, Kobayashi D, Matsui I, Fujii S, Biochemistry. 2012 May 8;51(18):3872-80. Epub 2012 Apr 23. PMID:22475127
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (3viv.pdb1.gz) 144 Kb
  • LPC: Ligand-Protein Contacts for 3VIV
  • CSU: Contacts of Structural Units for 3VIV
  • Structure Factors (405 Kb)
  • Retrieve 3VIV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VIV from S2C, [Save to disk]
  • Re-refined 3viv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VIV 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 3VIV
  • 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 3VIV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3viv] [3viv_B] [3viv_A] [3viv_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VIV
  • Community annotation for 3VIV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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