SMTL ID : 8cvs.1

Human PA200-20S proteasome with MG-132

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-1-mer

Ligands

6 x LDZ: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide(Non-covalent)

LDZ.1: 17 residues within 4Å: Chain H: T.1, T.21, E.22, A.27, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52, D.53 Chain I: D.125, L.126, I.127, C.129 15 PLIP interactions: 12 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:A.27, H:K.33, H:T.48, H:A.49, H:T.52, I:L.126, I:I.127 Hydrogen bonds: H:T.1, H:T.21, H:T.21, H:T.21, H:G.47, H:G.47, H:A.49, I:D.125 LDZ.2: 16 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.22, V.31, K.33, M.45, A.46, G.47, G.48, A.49, C.52 Chain L: Y.135, D.153, P.154 16 PLIP interactions: 12 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:A.22, K:V.31, K:M.45, K:A.49, L:Y.135, L:D.153, L:P.154 Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:T.21, K:K.33, K:K.33, K:G.47, K:A.49, L:D.153 LDZ.3: 15 residues within 4Å: Chain H: Y.114, H.116, S.118 Chain N: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52, M.95 12 PLIP interactions: 3 interactions with chain H, 9 interactions with chain N Hydrophobic interactions: H:Y.114, H:Y.114, N:T.20, N:T.22, N:K.33, N:T.52 pi-Stacking: H:H.116 Hydrogen bonds: N:T.1, N:T.21, N:T.21, N:G.47, N:A.49 LDZ.4: 16 residues within 4Å: Chain V: T.1, A.20, T.21, E.22, A.27, C.31, K.33, G.45, A.46, G.47, T.48, A.49 Chain W: D.125, L.126, I.127, C.129 13 PLIP interactions: 10 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:T.1, V:A.20, V:A.27, V:K.33, V:A.49, W:D.125, W:L.126, W:I.127 Hydrogen bonds: V:T.1, V:T.1, V:T.21, V:G.47, V:A.49 LDZ.5: 15 residues within 4Å: Chain Y: T.1, A.20, T.21, A.22, A.27, V.31, M.45, A.46, G.47, G.48, A.49 Chain Z: P.131, D.153, P.154, V.155 14 PLIP interactions: 6 interactions with chain Z, 8 interactions with chain Y Hydrophobic interactions: Z:P.131, Z:D.153, Z:P.154, Z:P.154, Z:V.155, Y:V.31, Y:V.31, Y:A.49 Hydrogen bonds: Z:D.153, Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:A.49 LDZ.6: 15 residues within 4Å: Chain 1: T.1, T.20, T.21, T.22, A.27, K.33, R.45, S.46, G.47, S.48, A.49, T.52 Chain V: Y.114, P.115, H.116 13 PLIP interactions: 11 interactions with chain 1, 2 interactions with chain V Hydrophobic interactions: 1:T.22, 1:T.22, 1:K.33, 1:R.45, 1:A.49, 1:T.52, V:Y.114, V:P.115 Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:G.47, 1:A.49

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.7: 13 residues within 4Å: Chain 2: K.156, K.1213, K.1216, H.1219, K.1271, Y.1286, K.1346, R.1350, R.1388, K.1391, H.1392, S.1434, R.1435 19 PLIP interactions: 19 interactions with chain 2 Hydrogen bonds: 2:Y.1286, 2:Y.1286 Salt bridges: 2:K.156, 2:K.156, 2:K.156, 2:K.1213, 2:K.1216, 2:K.1216, 2:K.1216, 2:K.1271, 2:K.1271, 2:K.1346, 2:K.1346, 2:R.1350, 2:R.1388, 2:K.1391, 2:K.1391, 2:H.1392, 2:R.1435 IHP.8: 9 residues within 4Å: Chain 2: Y.34, K.128, K.129, W.915, F.918, K.922, E.926, K.932, R.943 9 PLIP interactions: 9 interactions with chain 2 Hydrogen bonds: 2:Y.34, 2:R.943 Salt bridges: 2:K.128, 2:K.128, 2:K.129, 2:K.922, 2:K.922, 2:K.932, 2:R.943

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, J. et al., Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-11-02

Peptides

Proteasome subunit alpha type-2: AO
Proteasome subunit alpha type-4: BP
Proteasome subunit alpha type-7: CQ
Proteasome subunit alpha type-5: DR
Proteasome subunit alpha type-1: ES
Proteasome subunit alpha type-3: FT
Proteasome subunit alpha type-6: GU
Proteasome subunit beta type-7: HV
Proteasome subunit beta type-3: IW
Proteasome subunit beta type-2: JX
Proteasome subunit beta type-5: KY
Proteasome subunit beta type-1: LZ
Proteasome subunit beta type-4: M0
Proteasome subunit beta type-6: N1
Proteasome activator complex subunit 4: 2

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

2
c

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-5

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit alpha type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-5

Proteasome subunit beta type-1

Proteasome subunit beta type-4

Proteasome subunit beta type-6

Proteasome activator complex subunit 4

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