SMTL ID : 8f1f.1 (1 other biounit)

Structure of K48-linked tri-ubiquitin in complex with cyclic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: I.44, A.46, G.47, H.68 Chain B: Q.40 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.47, A:H.68, B:Q.40 Water bridges: A:A.46

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 6 residues within 4Å: Chain B: R.42, R.72 Chain D: Q.3, C.12, G.13, X.14 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.42, B:R.72 Hydrogen bonds: D:Q.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lemma, B. et al., Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation. Nat Commun (2023)

Release Date

2023-11-01

Peptides

Ubiquitin: A
Ubiquitin: B
Ubiquitin: C
Non-proteinogenic cyclic peptide (inhibitor): D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
1

Ubiquitin

Ubiquitin

Ubiquitin

Non-proteinogenic cyclic peptide (inhibitor)

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