SMTL ID : 5m32.1

Human 26S proteasome in complex with Oprozomib

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 x 6V9- 7C9- 7C9- 6VA: bound Oprozomib(Non-covalent)

6V9-7C9-7C9-6VA.1: 17 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, V.31, K.33, M.45, A.46, G.47, G.48, A.49, C.52, S.130, Y.169 Chain L: D.153, P.154, V.155 13 PLIP interactions: 3 interactions with chain L, 10 interactions with chain K Hydrophobic interactions: L:P.154, K:A.20, K:T.21, K:V.31, K:K.33, K:M.45, K:A.49 Hydrogen bonds: L:D.153, L:D.153, K:T.21, K:T.21, K:T.21, K:A.49 6V9-7C9-7C9-6VA.2: 16 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, V.31, K.33, M.45, A.46, G.47, A.49, C.52, S.130, Y.169 Chain Z: D.153, P.154, V.155 14 PLIP interactions: 2 interactions with chain Z, 12 interactions with chain Y Hydrophobic interactions: Z:P.154, Y:A.20, Y:T.21, Y:V.31, Y:K.33, Y:K.33, Y:M.45, Y:A.49 Hydrogen bonds: Z:D.153, Y:T.21, Y:T.21, Y:T.21, Y:G.48, Y:A.49

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.3: 17 residues within 4Å: Chain 2: D.176, V.177, G.178, G.179, P.218, G.219, T.220, G.221, K.222, T.223, I.354, H.358, G.382, A.383, R.386 Chain 3: R.343, R.346 9 PLIP interactions: 5 interactions with chain 2, 4 interactions with chain 3 Hydrogen bonds: 2:G.178, 2:G.179, 2:K.222, 2:T.223, 2:R.386 Salt bridges: 3:R.343, 3:R.343, 3:R.346, 3:R.346 ADP.4: 14 residues within 4Å: Chain 3: D.186, I.187, G.229, G.231, K.232, T.233, L.234, L.235, I.364, G.392, A.393, K.396 Chain 7: R.270, R.273 14 PLIP interactions: 9 interactions with chain 3, 5 interactions with chain 7 Hydrogen bonds: 3:D.186, 3:G.229, 3:G.231, 3:K.232, 3:T.233, 3:N.332, 3:K.396, 3:K.396, 7:R.270, 7:R.270, 7:R.273 pi-Cation interactions: 3:H.368 Salt bridges: 7:R.270, 7:R.270 ADP.5: 14 residues within 4Å: Chain 4: I.167, G.168, M.170, G.209, C.210, G.211, K.212, T.213, M.214, G.372, A.373 Chain 5: D.265, R.291, R.294 6 PLIP interactions: 3 interactions with chain 4, 3 interactions with chain 5 Hydrogen bonds: 4:G.168, 4:K.212, 4:T.213, 5:R.294 Salt bridges: 5:R.291, 5:R.291 ADP.6: 16 residues within 4Å: Chain 5: E.134, G.136, L.138, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316, G.340, A.341, R.344 Chain 6: R.344, R.347 13 PLIP interactions: 4 interactions with chain 6, 9 interactions with chain 5 Hydrogen bonds: 6:R.344, 5:G.136, 5:G.136, 5:G.177, 5:G.177, 5:G.179, 5:K.180, 5:T.181, 5:L.182, 5:H.316 Salt bridges: 6:R.344, 6:R.344, 6:R.347 ADP.7: 17 residues within 4Å: Chain 6: D.187, I.188, G.189, L.191, P.229, G.230, T.231, G.232, K.233, T.234, L.235, N.333, I.365, H.369, G.393, A.394, K.397 11 PLIP interactions: 9 interactions with chain 6, 2 interactions with chain 2 Hydrogen bonds: 6:G.189, 6:G.189, 6:T.231, 6:K.233, 6:T.234, 6:L.235, 6:N.333, 6:N.333 Salt bridges: 6:K.233, 2:R.333, 2:R.333 ADP.8: 16 residues within 4Å: Chain 7: M.113, I.114, G.115, P.155, G.156, T.157, G.158, K.159, T.160, L.161, E.213, I.291, H.295, G.319, A.320, K.323 9 PLIP interactions: 9 interactions with chain 7 Hydrogen bonds: 7:G.115, 7:G.156, 7:T.157, 7:T.157, 7:G.158, 7:K.159, 7:E.213, 7:K.323 Salt bridges: 7:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haselbach, D. et al., Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs. Nat Commun (2017)

Release Date

2017-07-05

Peptides

Proteasome subunit alpha type-2: AO
Proteasome subunit alpha type-4: BP
Proteasome subunit alpha type-7: C
Proteasome subunit alpha type-5: DR
Proteasome subunit alpha type-1: E
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 subunit alpha type-7: Q
Proteasome subunit alpha type-1: S
26S protease regulatory subunit 7: 2
26S protease regulatory subunit 4: 3
26S protease regulatory subunit 6B: 4
26S protease regulatory subunit 10B: 5
26S protease regulatory subunit 6A: 6
26S protease regulatory subunit 8: 7
26S proteasome non-ATPase regulatory subunit 1: 8
26S proteasome non-ATPase regulatory subunit 3: 9
26S proteasome non-ATPase regulatory subunit 12: a
26S proteasome non-ATPase regulatory subunit 11: b
26S proteasome non-ATPase regulatory subunit 6: c
26S proteasome non-ATPase regulatory subunit 7: d
26S proteasome non-ATPase regulatory subunit 13: e
26S proteasome non-ATPase regulatory subunit 4: f
26S proteasome non-ATPase regulatory subunit 14: g
26S proteasome non-ATPase regulatory subunit 8: h
26S proteasome complex subunit SEM1: i

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
O

B
B

P
P

C
C

D
D

R
R

E
E

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

Q
Q

S
S

2
c

3
d

4
e

5
f

6
g

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

g
q

h
r

i
s

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 subunit alpha type-7

Proteasome subunit alpha type-1

26S protease regulatory subunit 7

26S protease regulatory subunit 4

26S protease regulatory subunit 6B

26S protease regulatory subunit 10B

26S protease regulatory subunit 6A

26S protease regulatory subunit 8

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 3

26S proteasome non-ATPase regulatory subunit 12

26S proteasome non-ATPase regulatory subunit 11

26S proteasome non-ATPase regulatory subunit 6

26S proteasome non-ATPase regulatory subunit 7

26S proteasome non-ATPase regulatory subunit 13

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 8

26S proteasome complex subunit SEM1

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