SMTL ID : 8f7k.1

Thermoplasma acidophilum 20S proteasome - wild type bound to ZYA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-14-mer

Ligands

14 x XIB: N-[(benzyloxy)carbonyl]-L-tyrosyl-D-alanine(Non-covalent)

XIB.1: 19 residues within 4Å: Chain A: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 Chain U: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain U Hydrophobic interactions: A:A.27, A:K.30, A:K.30, A:L.78, A:V.79, U:V.21, U:A.151 Hydrogen bonds: A:S.32, A:G.77, A:V.79 Salt bridges: A:K.63 pi-Cation interactions: U:R.25 XIB.2: 19 residues within 4Å: Chain A: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain P: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain P Hydrophobic interactions: A:V.21, A:A.151, P:A.27, P:K.30, P:K.30, P:L.78, P:V.79 pi-Cation interactions: A:R.25 Hydrogen bonds: P:S.32, P:G.77, P:V.79 Salt bridges: P:K.63 XIB.3: 19 residues within 4Å: Chain P: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain Q: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 3 interactions with chain P, 9 interactions with chain Q Hydrophobic interactions: P:V.21, P:A.151, Q:A.27, Q:K.30, Q:K.30, Q:L.78, Q:V.79 pi-Cation interactions: P:R.25 Hydrogen bonds: Q:S.32, Q:G.77, Q:V.79 Salt bridges: Q:K.63 XIB.4: 19 residues within 4Å: Chain Q: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain R: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain R, 3 interactions with chain Q Hydrophobic interactions: R:A.27, R:K.30, R:K.30, R:L.78, R:V.79, Q:V.21, Q:A.151 Hydrogen bonds: R:S.32, R:G.77, R:V.79 Salt bridges: R:K.63 pi-Cation interactions: Q:R.25 XIB.5: 19 residues within 4Å: Chain R: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain S: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 3 interactions with chain R, 9 interactions with chain S Hydrophobic interactions: R:V.21, R:A.151, S:A.27, S:K.30, S:K.30, S:L.78, S:V.79 pi-Cation interactions: R:R.25 Hydrogen bonds: S:S.32, S:G.77, S:V.79 Salt bridges: S:K.63 XIB.6: 19 residues within 4Å: Chain S: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain T: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain T, 3 interactions with chain S Hydrophobic interactions: T:A.27, T:K.30, T:K.30, T:L.78, T:V.79, S:V.21, S:A.151 Hydrogen bonds: T:S.32, T:G.77, T:V.79 Salt bridges: T:K.63 pi-Cation interactions: S:R.25 XIB.7: 19 residues within 4Å: Chain T: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain U: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain U, 3 interactions with chain T Hydrophobic interactions: U:A.27, U:K.30, U:K.30, U:L.78, U:V.79, T:V.21, T:A.151 Hydrogen bonds: U:S.32, U:G.77, U:V.79 Salt bridges: U:K.63 pi-Cation interactions: T:R.25 XIB.8: 19 residues within 4Å: Chain 1: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain V: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain V, 3 interactions with chain 1 Hydrophobic interactions: V:A.27, V:K.30, V:K.30, V:L.78, V:V.79, 1:V.21, 1:A.151 Hydrogen bonds: V:S.32, V:G.77, V:V.79 Salt bridges: V:K.63 pi-Cation interactions: 1:R.25 XIB.9: 19 residues within 4Å: Chain V: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain W: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain W, 3 interactions with chain V Hydrophobic interactions: W:A.27, W:K.30, W:K.30, W:L.78, W:V.79, V:V.21, V:A.151 Hydrogen bonds: W:S.32, W:G.77, W:V.79 Salt bridges: W:K.63 pi-Cation interactions: V:R.25 XIB.10: 19 residues within 4Å: Chain W: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain X: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 3 interactions with chain W, 9 interactions with chain X Hydrophobic interactions: W:V.21, W:A.151, X:A.27, X:K.30, X:K.30, X:L.78, X:V.79 pi-Cation interactions: W:R.25 Hydrogen bonds: X:S.32, X:G.77, X:V.79 Salt bridges: X:K.63 XIB.11: 19 residues within 4Å: Chain X: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain Y: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain Y, 3 interactions with chain X Hydrophobic interactions: Y:A.27, Y:K.30, Y:K.30, Y:L.78, Y:V.79, X:V.21, X:A.151 Hydrogen bonds: Y:S.32, Y:G.77, Y:V.79 Salt bridges: Y:K.63 pi-Cation interactions: X:R.25 XIB.12: 19 residues within 4Å: Chain Y: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain Z: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain Z, 3 interactions with chain Y Hydrophobic interactions: Z:A.27, Z:K.30, Z:K.30, Z:L.78, Z:V.79, Y:V.21, Y:A.151 Hydrogen bonds: Z:S.32, Z:G.77, Z:V.79 Salt bridges: Z:K.63 pi-Cation interactions: Y:R.25 XIB.13: 19 residues within 4Å: Chain 0: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 Chain Z: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 12 PLIP interactions: 9 interactions with chain 0, 3 interactions with chain Z Hydrophobic interactions: 0:A.27, 0:K.30, 0:K.30, 0:L.78, 0:V.79, Z:V.21, Z:A.151 Hydrogen bonds: 0:S.32, 0:G.77, 0:V.79 Salt bridges: 0:K.63 pi-Cation interactions: Z:R.25 XIB.14: 19 residues within 4Å: Chain 0: G.16, R.17, L.18, V.21, E.22, R.25, A.151, T.153 Chain 1: A.27, K.30, G.31, S.32, K.63, T.75, S.76, G.77, L.78, V.79, A.80 12 PLIP interactions: 9 interactions with chain 1, 3 interactions with chain 0 Hydrophobic interactions: 1:A.27, 1:K.30, 1:K.30, 1:L.78, 1:V.79, 0:V.21, 0:A.151 Hydrogen bonds: 1:S.32, 1:G.77, 1:V.79 Salt bridges: 1:K.63 pi-Cation interactions: 0:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuah, J.J.Y. et al., High resolution structures define divergent and convergent mechanisms of archaeal proteasome activation. Commun Biol (2023)

Release Date

2023-08-30

Peptides

Proteasome subunit alpha: APQRSTUVWXYZ01
Proteasome subunit beta: BCDEFGHIJKLMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

P
B

Q
C

R
D

S
E

T
F

U
G

V
O

W
P

X
Q

Y
R

Z
S

0
T

1
U

B
H

C
I

D
J

E
K

F
L

G
M

H
N

I
V

J
W

K
X

L
Y

M
Z

N
a

O
b

Proteasome subunit alpha

Proteasome subunit beta

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