7K5J Signaling Protein date Sep 16, 2020
title Structure Of An E1-E2-Ubiquitin Thioester Mimetic
authors L.Yuan, Z.Lv, S.K.Olsen
compound source
Molecule: Ubiquitin
Chain: N, M, O, P, Q, R, W, X
Engineered: Yes
Organism_scientific: Triticum Aestivum
Organism_common: Wheat
Organism_taxid: 4565
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ubiquitin-Activating Enzyme E1 1
Chain: D, A, C, G, I, K, S, U
Ec: 6.2.1.45
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508
Gene: Uba1, Ykl210w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29ntev

Molecule: Ubiquitin-Conjugating Enzyme E2-34 Kda
Chain: F, B, E, H, J, L, T, V
Synonym: Cell Division Control Protein 34,E2 Ubiquitin-Conj Enzyme 3,E3 Ubiquitin Ligase Complex Scf Subunit Cdc34,Ubiq Carrier Protein,Ubiquitin-Protein Ligase;
Ec: 2.3.2.23
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508
Gene: Cdc34, Dna6, Ubc3, Ydr054c, D4211, Yd9609.08c
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29ntev
symmetry Space Group: P 1 21 1
R_factor 0.203 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.181 272.917 258.342 90.00 94.59 90.00
method X-Ray Diffractionresolution 3.42 Å
ligand AMP enzyme Ligase E.C.6.2.1.45 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3392 Kb) [Save to disk]
  • Biological Unit Coordinates (7k5j.pdb1.gz) 424 Kb
  • Biological Unit Coordinates (7k5j.pdb2.gz) 421 Kb
  • Biological Unit Coordinates (7k5j.pdb3.gz) 424 Kb
  • Biological Unit Coordinates (7k5j.pdb4.gz) 423 Kb
  • Biological Unit Coordinates (7k5j.pdb5.gz) 424 Kb
  • Biological Unit Coordinates (7k5j.pdb6.gz) 424 Kb
  • Biological Unit Coordinates (7k5j.pdb7.gz) 423 Kb
  • Biological Unit Coordinates (7k5j.pdb8.gz) 420 Kb
  • LPC: Ligand-Protein Contacts for 7K5J
  • CSU: Contacts of Structural Units for 7K5J
  • Structure Factors (1612 Kb)
  • Retrieve 7K5J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 7K5J from S2C, [Save to disk]
  • View 7K5J 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 7K5J
  • 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 7k5j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [7k5j_A] [7k5j_I] [7k5j_S] [7k5j_N] [7k5j_W] [7k5j_C] [7k5j_D] [7k5j_T] [7k5j_L] [7k5j_R] [7k5j_E] [7k5j_F] [7k5j_G] [7k5j_V] [7k5j_K] [7k5j_J] [7k5j_B] [7k5j_Q] [7k5j_U] [7k5j_H] [7k5j_X] [7k5j_P] [7k5j_M] [7k5j_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 7K5J
  • Community annotation for 7K5J at PDBWiki (http://pdbwiki.org)

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