SMTL ID : 8yvp.1

canine immunoproteasome 20S subunit in complex with compound 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x 01: [(2~{R},3~{R})-3-azanyl-4-oxidanyl-butan-2-yl]oxy-[(~{R})-cyclohexyl-[(1-cyclohexyl-1,2,3-triazol-4-yl)carbonylamino]methyl]-$l^{3}-oxidanyl-oxidanyl-boron

01.1: 10 residues within 4Å: Chain B: W.54, L.57, R.60, Y.89 Chain L: Y.124, R.127, F.128 Chain N: N.98, F.101, T.102 8 PLIP interactions: 4 interactions with chain L, 3 interactions with chain B, 1 interactions with chain N Hydrophobic interactions: L:Y.124, L:Y.124, L:R.127, L:F.128, B:L.57, B:Y.89, N:F.101 pi-Stacking: B:F.53 01.2: 18 residues within 4Å: Chain B: T.1, D.16, R.18, A.19, T.20, A.21, V.30, K.32, M.44, A.45, G.46, A.48, G.128, S.129, G.130, Y.168, S.169 Chain L: D.152 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.21, B:V.30, B:M.44, B:A.45, B:A.48 Hydrogen bonds: B:T.20, B:K.32, B:G.46, B:G.46, B:A.48, B:S.129, B:S.129, B:G.130 01.3: 19 residues within 4Å: Chain F: T.1, D.16, T.19, T.20, T.21, K.32, R.44, S.45, G.46, A.48, T.51, G.128, S.129, G.130, D.166, S.168, S.169 Chain K: Y.114, S.118 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain K Hydrophobic interactions: F:T.21, F:K.32, F:K.32, F:R.44, F:A.48, K:Y.114 Hydrogen bonds: F:T.1, F:T.20, F:K.32, F:G.46, F:G.46, F:A.48, F:S.129, F:S.129, F:G.130 01.4: 10 residues within 4Å: Chain G: Y.124, R.127, F.128 Chain H: W.54, L.57, R.60, Y.89 Chain W: N.98, F.101, T.102 8 PLIP interactions: 4 interactions with chain G, 1 interactions with chain W, 3 interactions with chain H Hydrophobic interactions: G:Y.124, G:Y.124, G:R.127, G:F.128, W:F.101, H:L.57, H:Y.89 pi-Stacking: H:F.53 01.5: 18 residues within 4Å: Chain G: D.152 Chain H: T.1, D.16, R.18, A.19, T.20, A.21, V.30, K.32, M.44, A.45, G.46, A.48, G.128, S.129, G.130, Y.168, S.169 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:A.21, H:V.30, H:M.44, H:A.45, H:A.48 Hydrogen bonds: H:T.20, H:K.32, H:G.46, H:G.46, H:A.48, H:S.129, H:S.129, H:G.130 01.6: 19 residues within 4Å: Chain A: Y.114, S.118 Chain Y: T.1, D.16, T.19, T.20, T.21, K.32, R.44, S.45, G.46, A.48, T.51, G.128, S.129, G.130, D.166, S.168, S.169 15 PLIP interactions: 14 interactions with chain Y, 1 interactions with chain A Hydrophobic interactions: Y:T.21, Y:K.32, Y:K.32, Y:R.44, Y:A.48, A:Y.114 Hydrogen bonds: Y:T.1, Y:T.20, Y:K.32, Y:G.46, Y:G.46, Y:A.48, Y:S.129, Y:S.129, Y:G.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arai, Y. et al., Optimization of alpha-amido boronic acids via cryo-electron microscopy analysis: Discovery of a novel highly selective immunoproteasome subunit LMP7 ( beta 5i)/LMP2 ( beta 1i) dual inhibitor. Bioorg.Med.Chem. (2024)

Release Date

2024-07-31

Peptides

Proteasome subunit beta type-7: AK
Proteasome subunit beta type-5: BH
Proteasome subunit alpha type-2: CP
Proteasome subunit alpha type-3: DI
Proteasome subunit alpha type-6: EO
Proteasome subunit beta type-6: FY
Proteasome subunit beta type-1: GL
Proteasome subunit beta type-3: J0
Proteasome subunit beta type-4: M1
Proteasome subunit alpha type-5: NW
Proteasome subunit beta type-2: QR
Proteasome subunit alpha type-7: SZ
Proteasome subunit alpha type-1: TV
Proteasome subunit alpha type-4: UX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

K
E

B
C

H
D

C
P

P
b

D
Q

I
J

E
R

O
K

F
F

Y
A

G
S

L
X

J
Y

0
U

M
a

1
W

N
H

W
M

Q
V

R
T

S
I

Z
N

T
L

V
G

U
O

X
Z

Proteasome subunit beta type-7

Proteasome subunit beta type-5

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-6

Proteasome subunit beta type-6

Proteasome subunit beta type-1

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit alpha type-5

Proteasome subunit beta type-2

Proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit alpha type-4

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