5B6C Hydrolase Protein Binding date May 26, 2016
title Structural Details Of Ufd1 Binding To P97
authors L.T.M.Le, J.K.Yang
compound source
Molecule: Transitional Endoplasmic Reticulum Atpase
Chain: A
Fragment: Unp Residues 21-191
Synonym: Ter Atpase,15s Mg(2+)-Atpase P97 Subunit,Valosin-C Protein,Vcp;
Ec: 3.6.4.6
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vcp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Peptide From Ubiquitin Fusion Degradation Protein Homolog;
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ufd1l
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: H 3
R_factor 0.158 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.270 107.270 44.040 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.55 Å
ligand
enzyme Hydrolase E.C.3.6.4.6 BRENDA
Primary referenceStructural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation., Le LT, Kang W, Kim JY, Le OT, Lee SY, Yang JK, PLoS One. 2016 Sep 29;11(9):e0163394. doi: 10.1371/journal.pone.0163394., eCollection 2016. PMID:27684549
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (5b6c.pdb1.gz) 35 Kb
  • CSU: Contacts of Structural Units for 5B6C
  • Structure Factors (567 Kb)
  • Retrieve 5B6C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B6C from S2C, [Save to disk]
  • Re-refined 5b6c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B6C 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 5B6C
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5b6c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b6c_A] [5b6c] [5b6c_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5B6C
  • Community annotation for 5B6C at PDBWiki (http://pdbwiki.org)

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