SMTL ID : 9b5l.1

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 15 residues within 4Å: Chain A: A.424, G.425, D.452, M.453, D.454, R.463, K.476, R.501, V.502, A.524, L.525, D.526, N.527, A.530 Chain B: G.76 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.424, A:D.454, A:D.454, A:K.476, A:K.476, A:V.502, A:V.502, A:D.526, A:N.527 Salt bridges: A:R.463

1 x 01: 4-aminobutanenitrile

01.2: 7 residues within 4Å: Chain A: P.580, I.581, C.582 Chain C: C.85, L.86, D.117 Chain D: G.79 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:L.86, 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
Polyubiquitin: 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

Polyubiquitin

Ubiquitin-conjugating enzyme E2 4

Ubiquitin

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