SMTL ID : 8g6e.1

Structure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x YRE: (7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyrrolidin-1-yl)-2-oxa-8,11-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-7-carboxamide(Non-covalent)

YRE.1: 11 residues within 4Å: Chain C: R.96, Y.99, N.100 Chain J: T.64, I.68, Y.71, Y.105 Chain K: K.87, A.90, Y.91, R.95 11 PLIP interactions: 5 interactions with chain C, 3 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: C:R.96, C:Y.99, C:Y.99, C:Y.99, J:I.68, J:I.68, J:Y.71, K:Y.91 Hydrogen bonds: C:N.100, K:R.95, K:R.95 YRE.2: 19 residues within 4Å: Chain I: T.1, R.19, A.20, T.21, E.22, A.27, C.31, G.45, G.47, V.48, A.49, L.52 Chain J: A.136, Y.137, D.138, I.140, A.142, K.143, C.144 13 PLIP interactions: 3 interactions with chain J, 10 interactions with chain I Hydrophobic interactions: J:I.140, I:A.20, I:E.22, I:V.48, I:L.52 Hydrogen bonds: J:D.138, I:T.21, I:T.21, I:G.47, I:A.49 Salt bridges: J:D.138, I:E.22 Water bridges: I:G.50 YRE.3: 20 residues within 4Å: Chain L: T.1, R.19, A.20, S.21, M.22, S.27, M.45, G.47, G.48, A.49, D.51, C.96 Chain M: R.128, F.135, N.151, D.153, S.154, S.157, Y.158, C.159 14 PLIP interactions: 9 interactions with chain L, 5 interactions with chain M Hydrophobic interactions: L:A.20, L:M.45, M:F.135 Hydrogen bonds: L:S.21, L:S.21, L:S.27, L:G.47, L:A.49, M:D.153, M:D.153, M:S.154, M:S.157 Water bridges: L:T.1, L:A.50 YRE.4: 10 residues within 4Å: Chain Q: R.96, Y.99, N.100 Chain X: T.64, I.68, Y.71, Y.105 Chain Y: A.90, Y.91, R.95 11 PLIP interactions: 5 interactions with chain Q, 3 interactions with chain Y, 3 interactions with chain X Hydrophobic interactions: Q:R.96, Q:Y.99, Q:Y.99, Q:Y.99, Y:Y.91, X:I.68, X:I.68, X:Y.71 Hydrogen bonds: Q:N.100, Y:R.95, Y:R.95 YRE.5: 17 residues within 4Å: Chain W: T.1, R.19, A.20, T.21, E.22, A.27, C.31, G.47, V.48, A.49, L.52 Chain X: A.136, Y.137, D.138, A.142, K.143, C.144 13 PLIP interactions: 11 interactions with chain W, 2 interactions with chain X Hydrophobic interactions: W:A.20, W:V.48, W:A.49, W:L.52 Hydrogen bonds: W:T.21, W:T.21, W:G.47, W:A.49, X:D.138 Water bridges: W:G.23, W:G.50 Salt bridges: W:E.22, X:D.138 YRE.6: 20 residues within 4Å: Chain 0: R.128, F.135, N.151, D.153, S.154, S.157, Y.158, C.159 Chain Z: T.1, R.19, A.20, S.21, M.22, S.27, M.45, G.47, G.48, A.49, D.51, C.96 15 PLIP interactions: 6 interactions with chain 0, 9 interactions with chain Z Hydrophobic interactions: 0:F.135, Z:A.20, Z:M.45 Hydrogen bonds: 0:N.151, 0:D.153, 0:D.153, 0:S.154, 0:S.157, Z:S.21, Z:S.21, Z:S.27, Z:G.47, Z:A.49 Water bridges: Z:T.1, Z:A.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsu, H.C. et al., Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors. Nat Commun (2023)

Release Date

2023-12-20

Peptides

Proteasome subunit alpha type-6: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type: CQ
Proteasome subunit alpha type: DR
Proteasome subunit alpha type: ES
Proteasome subunit alpha type-1: FT
Proteasome subunit alpha type-3: GU
Proteasome subunit beta type-6: HV
Proteasome subunit beta: IW
Proteasome subunit beta: JX
Proteasome subunit beta: KY
Proteasome subunit beta: LZ
Proteasome subunit beta: M0
Proteasome subunit beta: N1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
O

B
B

P
P

C
C

Q
Q

D
D

R
R

E
E

S
S

F
F

T
T

G
G

U
U

H
H

V
V

I
I

W
W

J
J

X
X

K
K

Y
Y

L
L

Z
Z

M
M

0
a

N
N

1
b

Proteasome subunit alpha type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type

Proteasome subunit alpha type

Proteasome subunit alpha type

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit beta type-6

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit beta

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