SMTL ID : 8ypk.1

mouse proteasome 20S subunit in complex with compound 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

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

Ligands

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

01.1: 19 residues within 4Å: Chain A: T.1, D.16, T.19, T.20, T.21, K.32, R.44, S.45, G.46, S.47, A.48, T.51, G.127, G.128, S.129, G.130, S.168, S.169 Chain Q: Y.114 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain Q Hydrophobic interactions: A:T.21, A:R.44, Q:Y.114 Hydrogen bonds: A:T.20, A:K.32, A:G.46, A:G.46, A:A.48, A:S.129, A:S.129, A:G.130, A:D.166, A:S.168 01.2: 17 residues within 4Å: Chain G: T.1, D.16, R.18, A.19, T.20, V.30, K.32, M.44, A.45, G.46, A.48, V.127, G.128, S.129, G.130, Y.168, S.169 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:V.30, G:K.32, G:M.44, G:A.45, G:A.48 Hydrogen bonds: G:R.18, G:T.20, G:K.32, G:G.46, G:G.46, G:A.48, G:S.129, G:S.129, G:G.130 01.3: 18 residues within 4Å: Chain N: T.1, D.16, R.18, A.19, T.20, V.30, K.32, M.44, A.45, G.46, G.47, A.48, V.127, G.128, S.129, G.130, Y.168, S.169 14 PLIP interactions: 14 interactions with chain N Hydrophobic interactions: N:V.30, N:K.32, N:M.44, N:A.45, N:A.48 Hydrogen bonds: N:R.18, N:T.20, N:K.32, N:G.46, N:G.46, N:A.48, N:S.129, N:S.129, N:G.130 01.4: 19 residues within 4Å: Chain T: Y.114 Chain X: T.1, D.16, T.19, T.20, T.21, K.32, R.44, S.45, G.46, S.47, A.48, T.51, G.127, G.128, S.129, G.130, S.168, S.169 13 PLIP interactions: 12 interactions with chain X, 1 interactions with chain T Hydrophobic interactions: X:T.21, X:R.44, T:Y.114 Hydrogen bonds: X:T.20, X:K.32, X:G.46, X:G.46, X:A.48, X:S.129, X:S.129, X:G.130, X:D.166, X:S.168

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-6: AX
Proteasome subunit alpha type-2: BK
Proteasome subunit alpha type-7: CP
Proteasome subunit alpha type-6: DI
Proteasome subunit beta type-2: EJ
Proteasome subunit beta type-1: F1
Proteasome subunit beta type-5: GN
Proteasome subunit alpha type-3: HV
Proteasome subunit alpha type-1: LU
Proteasome subunit alpha type-5: MR
Proteasome subunit alpha type-4: OY
Proteasome subunit beta type-7: QT
Proteasome subunit beta type-4: SW
Proteasome subunit beta type-3: Z0

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

X
F

B
P

K
b

C
N

P
I

D
R

I
K

E
T

J
V

F
S

1
X

G
D

N
C

H
J

V
Q

L
L

U
G

M
H

R
M

O
O

Y
Z

Q
B

T
E

S
W

W
a

Z
Y

0
U

Proteasome subunit beta type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type-7

Proteasome subunit alpha type-6

Proteasome subunit beta type-2

Proteasome subunit beta type-1

Proteasome subunit beta type-5

Proteasome subunit alpha type-3

Proteasome subunit alpha type-1

Proteasome subunit alpha type-5

Proteasome subunit alpha type-4

Proteasome subunit beta type-7

Proteasome subunit beta type-4

Proteasome subunit beta type-3

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