SMTL ID : 9b5k.1

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (Ub(A)/ATP/Mg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.526 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.526 MG.2: 3 residues within 4Å: Chain A: D.454, K.476 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.454

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 19 residues within 4Å: Chain A: R.11, G.425, D.452, M.453, D.454, N.460, R.463, Q.464, K.476, R.501, V.502, A.524, L.525, D.526, N.527, A.530 Chain B: G.76 Ligands: MG.1, MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.454, A:N.460, A:Q.464, A:K.476, A:V.502, A:V.502, A:N.527 Salt bridges: A:R.11, A:R.463, A:R.463, A:K.476, A:K.476

1 x 01: 4-aminobutanenitrile

01.4: 7 residues within 4Å: Chain A: P.580, I.581, C.582 Chain C: C.85, D.117 Chain D: R.78, G.79 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.117, A:I.581

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kochanczyk, T. et al., Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature (2024)

Release Date

2024-06-05

Peptides

Ubiquitin-activating enzyme E1 1: A
Large ribosomal subunit protein eL40B: B
Ubiquitin-conjugating enzyme E2 4: C
Ubiquitin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ubiquitin-activating enzyme E1 1

Large ribosomal subunit protein eL40B

Ubiquitin-conjugating enzyme E2 4

Ubiquitin

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