SMTL ID : 9g7g.1

Structure of the clippase PaJOS from Pigmentiphaga aceris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-12-12-mer

Ligands

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

AYE.1: 7 residues within 4Å: Chain A: Q.61, S.64, C.66, D.186, H.187 Chain B: R.74, G.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.186 AYE.2: 6 residues within 4Å: Chain C: S.64, C.66, D.186, H.187 Chain D: R.74, G.75 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.186 AYE.3: 7 residues within 4Å: Chain E: Q.61, S.64, C.66, D.186, H.187 Chain F: R.74, G.75 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.186 AYE.4: 7 residues within 4Å: Chain G: Q.61, S.64, C.66, D.186, H.187 Chain H: R.74, G.75 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.186 AYE.5: 7 residues within 4Å: Chain I: Q.61, S.64, C.66, D.186, H.187 Chain J: R.74, G.75 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.186 AYE.6: 7 residues within 4Å: Chain K: Q.61, S.64, C.66, D.186, H.187 Chain L: R.74, G.75 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.186 AYE.7: 7 residues within 4Å: Chain M: Q.61, S.64, C.66, D.186, H.187 Chain N: R.74, G.75 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:D.186 AYE.8: 7 residues within 4Å: Chain O: Q.61, S.64, C.66, D.186, H.187 Chain P: R.74, G.75 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:D.186 Water bridges: O:A.67 AYE.9: 7 residues within 4Å: Chain Q: Q.61, S.64, C.66, D.186, H.187 Chain R: R.74, G.75 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:D.186 AYE.10: 7 residues within 4Å: Chain S: Q.61, S.64, C.66, D.186, H.187 Chain T: R.74, G.75 1 PLIP interactions: 1 interactions with chain S Hydrogen bonds: S:D.186 AYE.11: 7 residues within 4Å: Chain U: Q.61, S.64, C.66, D.186, H.187 Chain V: R.74, G.75 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:D.186 AYE.12: 7 residues within 4Å: Chain W: Q.61, S.64, C.66, D.186, H.187 Chain X: R.74, G.75 2 PLIP interactions: 2 interactions with chain W Hydrogen bonds: W:D.186 Water bridges: W:A.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hermanns, T. et al., A family of bacterial Josephin-like deubiquitinases with an irreversible cleavage mode. Mol.Cell (2025)

Release Date

2025-04-23

Peptides

PaJOS: ACEGIKMOQSUW
Polyubiquitin-B: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

S
S

U
U

W
W

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

PaJOS

Polyubiquitin-B

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