5C1B Hydrolase date Jun 13, 2015
title P97-Delta709-728 In Complex With A Ufd1-Shp Peptide
authors P.Haenzelmann, H.Schindelin
compound source
Molecule: Transitional Endoplasmic Reticulum Atpase
Chain: A, B, C, D, E, F
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: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_vector_type: Plasmid

Molecule: Ubiquitin Fusion Degradation Protein 1 Homolog
Chain: V, U
Fragment: Unp Residues 221-241
Synonym: Ub Fusion Protein 1
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: This Sequence Occurs Naturally In Humans
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
140.715 180.664 254.958 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.08 Å
ligand AGS, CL, GOL, MG enzyme Hydrolase E.C.3.6.4.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • deubiquitinase activator act...


  • Primary referenceCharacterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions., Hanzelmann P, Schindelin H, Structure. 2016 Jan 5;24(1):140-7. doi: 10.1016/j.str.2015.10.027. Epub 2015 Dec , 17. PMID:26712280
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2212 Kb) [Save to disk]
  • Biological Unit Coordinates (5c1b.pdb1.gz) 2194 Kb
  • LPC: Ligand-Protein Contacts for 5C1B
  • CSU: Contacts of Structural Units for 5C1B
  • Structure Factors (6541 Kb)
  • Retrieve 5C1B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C1B from S2C, [Save to disk]
  • Re-refined 5c1b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C1B 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 5C1B
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5c1b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c1b_B] [5c1b_D] [5c1b_A] [5c1b_V] [5c1b_U] [5c1b] [5c1b_C] [5c1b_F] [5c1b_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5C1B: [AAA] [CDC48_2] [CDC48_N ] by SMART
  • Other resources with information on 5C1B
  • Community annotation for 5C1B at PDBWiki (http://pdbwiki.org)

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