SMTL ID : 5lez.1

Human 20S proteasome complex with Oprozomib in Mg-Acetate at 2.2 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

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

Ligands

4 x 6V9- OAS- OAS- 6VA: bound Oprozomib(Non-covalent)

6V9-OAS-OAS-6VA.1: 18 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.22, A.27, V.31, K.33, M.45, A.46, G.47, A.49, S.130, Y.169 Chain L: D.125, P.126, V.127 Ligands: ACT.30 14 PLIP interactions: 12 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:A.20, K:V.31, K:M.45, K:A.49 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49, L:D.125, L:D.125 Water bridges: K:G.23, K:A.50 6V9-OAS-OAS-6VA.2: 18 residues within 4Å: Chain H: Y.114, H.116 Chain N: T.1, R.19, T.20, T.21, T.22, T.31, K.33, R.45, S.46, G.47, S.48, A.49, Q.53, S.130, S.169 Ligands: ACT.31 13 PLIP interactions: 13 interactions with chain N Hydrophobic interactions: N:T.31, N:K.33, N:R.45, N:A.49 Hydrogen bonds: N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49 Water bridges: N:T.21, N:G.23, N:A.50 6V9-OAS-OAS-6VA.3: 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, S.130, Y.169 Chain Z: D.125, P.126, V.127 Ligands: ACT.32 17 PLIP interactions: 15 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.20, Y:V.31, Y:M.45, Y:A.49 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:D.125 Water bridges: Y:T.21, Y:T.21, Y:G.23, Y:G.23, Y:A.50, Z:S.129 6V9-OAS-OAS-6VA.4: 18 residues within 4Å: Chain 1: T.1, R.19, T.20, T.21, T.22, T.31, K.33, R.45, S.46, G.47, S.48, A.49, Q.53, S.130, S.169 Chain V: Y.114, H.116 Ligands: ACT.33 11 PLIP interactions: 11 interactions with chain 1 Hydrophobic interactions: 1:T.20, 1:T.31, 1:K.33, 1:A.49 Hydrogen bonds: 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:G.47, 1:A.49 Water bridges: 1:A.50

6 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain G: T.14, Y.125, N.128, A.129, M.131 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:T.14, G:Y.125, G:N.128, G:M.131, H2O.31 K.16: 5 residues within 4Å: Chain L: A.183, D.186, V.187, T.189, D.213 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:A.183, L:D.186, L:T.189, H2O.60 K.19: 4 residues within 4Å: Chain N: R.19, M.164, D.167, S.170 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:M.164, N:D.167, N:S.170, H2O.74, H2O.75 K.21: 4 residues within 4Å: Chain U: T.14, Y.125, N.128, M.131 5 PLIP interactions: 4 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:T.14, U:Y.125, U:N.128, U:M.131, H2O.103 K.27: 4 residues within 4Å: Chain Z: A.183, D.186, V.187, T.189 4 PLIP interactions: 3 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: Z:A.183, Z:D.186, Z:T.189, H2O.126 K.29: 4 residues within 4Å: Chain 1: R.19, M.164, D.167, S.170 5 PLIP interactions: 3 interactions with chain 1, 2 Ligand-Water interactions Metal complexes: 1:M.164, 1:D.167, 1:S.170, H2O.142, H2O.142

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.6: 3 residues within 4Å: Chain H: Q.91 Chain N: D.51, D.93 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain H: I.163, D.166, S.169 Chain Z: D.213 5 PLIP interactions: 1 interactions with chain Z, 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: Z:D.213, H:I.163, H:D.166, H:S.169, H2O.129 MG.9: 3 residues within 4Å: Chain I: V.175, D.178, S.181 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:V.175, I:D.178, I:S.181, H2O.43, H2O.46 MG.11: 6 residues within 4Å: Chain I: D.205 Chain Y: R.19, T.164, D.167, A.168, S.170 5 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: Y:T.164, Y:D.167, Y:S.170, I:D.205, H2O.47 MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 6 residues within 4Å: Chain K: R.19, T.164, D.167, A.168, S.170 Chain W: D.205 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: K:T.164, K:D.167, K:S.170, W:D.205, H2O.57 MG.17: 4 residues within 4Å: Chain L: D.213 Chain V: I.163, D.166, S.169 5 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: V:I.163, V:D.166, V:S.169, L:D.213, H2O.108 MG.22: 3 residues within 4Å: Chain 1: D.51, D.93 Chain V: Q.91 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain W: V.175, D.178, S.181 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:V.175, W:D.178, W:S.181, H2O.112, H2O.112 MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

9 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 3 residues within 4Å: Chain H: Y.90 Chain I: Y.96, E.97 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:Y.90 Water bridges: I:Y.96 1PE.10: 4 residues within 4Å: Chain I: R.66, E.97, K.98 Chain J: D.90 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:K.98 Water bridges: I:R.70 1PE.14: 4 residues within 4Å: Chain D: N.98 Chain K: Y.90 Chain L: S.98, F.101 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.98 1PE.15: 4 residues within 4Å: Chain 1: T.22 Chain L: F.33 Chain M: Y.144 Chain V: S.129 1 PLIP interactions: 1 interactions with chain V Water bridges: V:S.129 1PE.18: 7 residues within 4Å: Chain G: Y.103 Chain H: F.88, R.89, Q.91 Chain N: A.54, Y.90, L.94 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:Y.103, H:R.89 1PE.20: 8 residues within 4Å: Chain 1: A.58, Y.61, Y.90, L.94 Chain U: Y.103 Chain V: F.88, R.89, Q.91 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain 1 Hydrogen bonds: V:R.89, V:Q.91 Water bridges: 1:A.58 1PE.24: 5 residues within 4Å: Chain W: R.66, E.97, K.98, G.101 Chain X: D.90 4 PLIP interactions: 1 interactions with chain X, 3 interactions with chain W Hydrogen bonds: X:D.90, W:R.66, W:K.98 Water bridges: W:G.101 1PE.26: 6 residues within 4Å: Chain R: N.98 Chain Y: F.54, Y.90 Chain Z: Y.97, S.98, F.101 No protein-ligand interaction detected (PLIP) 1PE.28: 5 residues within 4Å: Chain 0: Y.141, Y.144 Chain H: S.129 Chain N: T.22 Chain Z: F.33 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.30: 5 residues within 4Å: Chain K: T.1, G.47, G.129, S.130 Ligands: 6V9-OAS-OAS-6VA.1 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.47, K:S.130 ACT.31: 6 residues within 4Å: Chain N: T.1, S.46, G.47, G.129, S.130 Ligands: 6V9-OAS-OAS-6VA.2 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:G.47, N:S.130 ACT.32: 5 residues within 4Å: Chain Y: T.1, G.47, G.129, S.130 Ligands: 6V9-OAS-OAS-6VA.3 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:G.47, Y:S.130 ACT.33: 6 residues within 4Å: Chain 1: T.1, S.46, G.47, G.129, S.130 Ligands: 6V9-OAS-OAS-6VA.4 3 PLIP interactions: 3 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:G.47, 1:S.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schrader, J. et al., The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design. Science (2016)

Release Date

2016-08-17

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

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-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

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