6DC6 Signaling Protein Ligase date May 04, 2018
title Crystal Structure Of Human Ubiquitin Activating Enzyme E1 (U Complex With Ubiquitin
authors Z.Lv, L.Yuan, K.M.Williams, J.H.Atkison, S.K.Olsen
compound source
Molecule: Ubiquitin-Like Modifier-Activating Enzyme 1
Chain: A, C
Synonym: Protein A1s9,Ubiquitin-Activating Enzyme E1
Ec: 6.2.1.45
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Uba1, A1s9t, Ube1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfastbac-Htb

Molecule: Ubiquitin
Chain: B, D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29-Ntev
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.999 70.438 188.851 90.00 95.19 90.00
method X-Ray Diffractionresolution 3.14 Å
ligand
enzyme Ligase E.C.6.2.1.45 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceCrystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity., Lv Z, Williams KM, Yuan L, Atkison JH, Olsen SK, J Biol Chem. 2018 Oct 2. pii: RA118.003975. doi: 10.1074/jbc.RA118.003975. PMID:30279270
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (744 Kb) [Save to disk]
  • Biological Unit Coordinates (6dc6.pdb1.gz) 365 Kb
  • Biological Unit Coordinates (6dc6.pdb2.gz) 371 Kb
  • CSU: Contacts of Structural Units for 6DC6
  • Structure Factors (312 Kb)
  • Retrieve 6DC6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DC6 from S2C, [Save to disk]
  • View 6DC6 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 6DC6
  • 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 6dc6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6dc6_D] [6dc6_A] [6dc6_C] [6dc6_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6DC6
  • Community annotation for 6DC6 at PDBWiki (http://pdbwiki.org)

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