SMTL ID : 8c61.2 (1 other biounit)

Structure of USP54 in complex with Lys63-linked diUbiquitin-PA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.48, C.50, C.55, C.58 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.48, A:C.50, A:C.55, A:C.58 ZN.2: 4 residues within 4Å: Chain A: H.114, C.126, C.131, H.134 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.114, A:C.126, A:C.131, A:H.134 ZN.3: 4 residues within 4Å: Chain A: C.147, C.150, C.206, C.210 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.147, A:C.150, A:C.206, A:C.210 ZN.6: 4 residues within 4Å: Chain D: H.48, C.50, C.55, C.58 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.48, D:C.50, D:C.55, D:C.58 ZN.7: 4 residues within 4Å: Chain D: H.114, C.126, C.131, H.134 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.114, D:C.126, D:C.131, D:H.134 ZN.8: 4 residues within 4Å: Chain D: C.147, C.150, C.206, C.210 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.147, D:C.150, D:C.206, D:C.210

2 x AYE: prop-2-en-1-amine(Covalent)

AYE.4: 8 residues within 4Å: Chain A: N.16, N.21, S.22, C.23, M.99, K.282, H.283 Chain B: G.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.282 AYE.9: 8 residues within 4Å: Chain D: N.16, N.21, S.22, C.23, M.99, K.282, H.283 Chain E: G.75 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.282

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: L.273, F.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wendrich, K. et al., Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53. Nat.Chem.Biol. (2024)

Release Date

2024-07-31

Peptides

Inactive ubiquitin carboxyl-terminal hydrolase 54: AD
Polyubiquitin-B: BE
Ubiquitin: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

D
J

B
H

E
K

C
I

F
L

Inactive ubiquitin carboxyl-terminal hydrolase 54

Polyubiquitin-B

Ubiquitin

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