5KIY Hydrolase Membrane Protein date Jun 17, 2016
title P97 Nd1-A232e In Complex With Vimp
authors W.K.Tang, D.Xia
compound source
Molecule: Transitional Endoplasmic Reticulum Atpase
Chain: A
Fragment: N-Terminal Residues 1-460
Synonym: Ter Atpase,15s Mg(2+)-Atpase P97 Subunit,Valosin-C Protein,Vcp;
Ec: 3.6.4.6
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vcp
Expression_system: Bacteria
Expression_system_taxid: 2

Molecule: Selenoprotein S
Chain: B
Fragment: Residues 49-122
Synonym: Sels,Vcp-Interacting Membrane Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Selenos, Sels, Vimp, Ad-015, Sbbi8
Expression_system: Bacteria
Expression_system_taxid: 2
symmetry Space Group: P 6 2 2
R_factor 0.193 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.998 144.998 119.817 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.79 Å
ligand ANP, MG enzyme Hydrolase E.C.3.6.4.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis for nucleotide-modulated p97 association with the ER membrane., Tang WK, Zhang T, Ye Y, Xia D, Cell Discov. 2017 Dec 12;3:17045. doi: 10.1038/celldisc.2017.45. eCollection, 2017. PMID:29238611
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (5kiy.pdb1.gz) 941 Kb
  • LPC: Ligand-Protein Contacts for 5KIY
  • CSU: Contacts of Structural Units for 5KIY
  • Structure Factors (402 Kb)
  • Retrieve 5KIY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KIY from S2C, [Save to disk]
  • View 5KIY 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 5KIY
  • 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: [5kiy_B] [5kiy_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KIY
  • Community annotation for 5KIY at PDBWiki (http://pdbwiki.org)

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