SMTL ID : 9fsv.1

Yeast 20S proteasome with human beta2i (1-53) in complex with epoxyketone inhibitor 42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

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

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134 MG.5: 4 residues within 4Å: Chain I: A.175, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.175, I:D.178, I:S.181 MG.6: 7 residues within 4Å: Chain K: R.18, A.164, H.165, D.167, A.168, S.170 Chain W: D.205 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.164, K:D.167, K:S.170, W:D.205 MG.10: 5 residues within 4Å: Chain 0: L.47 Chain N: R.19, I.163, D.166, S.169 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:I.163, N:S.169 MG.14: 7 residues within 4Å: Chain L: D.222 Chain V: R.18, I.162, W.163, D.165, L.166, S.168 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.162, V:D.165, V:S.168, L:D.222 MG.17: 4 residues within 4Å: Chain W: A.175, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:A.175, W:D.178, W:S.181 MG.18: 7 residues within 4Å: Chain I: D.205 Chain Y: R.18, A.164, H.165, D.167, A.168, S.170 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.164, Y:D.167, Y:S.170, I:D.205 MG.22: 6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.68 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain N: T.31, R.45, Q.53 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.68 Ligand excluded by PLIP

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 5 residues within 4Å: Chain H: G.46, G.127, S.128 Chain Z: Y.33 Ligands: 01.4 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.46, H:S.128 MES.7: 10 residues within 4Å: Chain J: R.23 Chain K: G.46, S.95, M.96, G.97, D.115, G.129, S.130 Ligands: SO4.8, 01.9 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.46, K:S.130 MES.15: 6 residues within 4Å: Chain L: Y.33 Chain V: A.45, G.46, G.127, S.128 Ligands: 01.16 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:G.46, V:S.128 MES.19: 11 residues within 4Å: Chain X: R.23 Chain Y: G.46, S.95, M.96, G.97, D.115, V.128, G.129, S.130 Ligands: SO4.20, 01.21 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:G.46, Y:S.130

4 x 01: (2S)-N-[(2S)-1-[[(1S)-2-cyclohexyl-1-[(2R,3S,6R,7S)-3-methanoyl-2,6-dimethyl-6,7-bis(oxidanyl)-1,4-oxazepan-7-yl]ethyl]amino]-3-(4-methoxyphenyl)-1-oxidanylidene-propan-2-yl]-2-(2-morpholin-4-ylethanoylamino)-4-oxidanyl-butanamide

01.4: 24 residues within 4Å: Chain H: T.1, I.2, D.16, R.18, A.19, T.20, N.21, A.26, C.30, K.32, G.44, A.45, G.46, V.47, A.48, L.126, G.127, S.128, G.129, G.167, S.168 Chain I: D.125, L.126 Ligands: MES.3 19 PLIP interactions: 16 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:I.2, H:K.32, H:A.45 Hydrogen bonds: H:T.1, H:T.20, H:T.20, H:K.32, H:G.46, H:G.46, H:G.46, H:A.48, H:S.128, H:S.128, H:S.128, H:G.129, H:S.168, I:D.125, I:D.125 Salt bridges: I:D.125 01.9: 23 residues within 4Å: Chain K: T.1, T.2, D.16, R.18, A.19, T.20, A.26, V.30, K.32, M.44, A.45, G.46, G.47, A.48, G.129, S.130, G.131, Y.169, S.170 Chain L: D.126, V.128 Ligands: MES.7, SO4.8 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:T.2, K:T.20, K:V.30, K:K.32, K:A.45, K:A.48 Hydrogen bonds: K:T.20, K:T.20, K:T.20, K:K.32, K:G.46, K:G.46, K:G.46, K:A.48, K:G.131, L:D.126 Water bridges: K:A.49 Salt bridges: L:D.126 01.16: 25 residues within 4Å: Chain V: T.1, I.2, D.16, A.19, T.20, N.21, A.26, C.30, K.32, H.34, G.44, A.45, G.46, V.47, A.48, E.52, L.126, G.127, S.128, G.129, G.167, S.168 Chain W: D.125, L.126 Ligands: MES.15 18 PLIP interactions: 15 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:I.2, V:K.32, V:K.32, V:A.45, V:V.47, V:A.48 Hydrogen bonds: V:T.1, V:T.20, V:T.20, V:K.32, V:G.46, V:G.46, V:G.46, V:A.48, V:G.129, W:D.125, W:D.125 Salt bridges: W:D.125 01.21: 25 residues within 4Å: Chain Y: T.1, T.2, D.16, R.18, A.19, T.20, A.26, V.30, K.31, K.32, M.44, A.45, G.46, G.47, A.48, S.95, V.128, G.129, S.130, G.131, Y.169, S.170 Chain Z: D.126 Ligands: MES.19, SO4.20 17 PLIP interactions: 15 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:T.2, Y:T.20, Y:V.30, Y:K.32, Y:M.44, Y:A.45 Hydrogen bonds: Y:T.20, Y:T.20, Y:K.32, Y:G.46, Y:G.46, Y:G.46, Y:A.48, Y:S.130, Y:G.131, Z:D.126 Salt bridges: Z:D.126

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain K: T.20, Y.169 Ligands: MES.7, 01.9 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.20 SO4.11: 5 residues within 4Å: Chain N: T.1, S.46, G.47, G.128, S.129 5 PLIP interactions: 5 interactions with chain N Hydrogen bonds: N:T.1, N:T.1, N:G.47, N:S.129, N:S.129 SO4.20: 4 residues within 4Å: Chain Y: T.20, Y.169 Ligands: MES.19, 01.21 1 PLIP interactions: 1 interactions with chain Y Hydrogen bonds: Y:T.20 SO4.23: 5 residues within 4Å: Chain 1: T.1, S.46, G.47, G.128, S.129 5 PLIP interactions: 5 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:T.1, 1:T.1, 1:G.47, 1:S.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurits, E. et al., Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites. to be published

Release Date

2024-07-17

Peptides

Proteasome subunit alpha type-2: AO
Proteasome subunit alpha type-3: BP
Proteasome subunit alpha type-4: CQ
Proteasome subunit alpha type-5: DR
Proteasome subunit alpha type-6: ES
Probable proteasome subunit alpha type-7: FT
Proteasome subunit alpha type-1: GU
Proteasome subunit beta type-10,Proteasome subunit beta type-2: HV
Proteasome subunit beta type-3: IW
Proteasome subunit beta type-4: JX
Proteasome subunit beta type-5: KY
Proteasome subunit beta type-6: LZ
Proteasome subunit beta type-7: M0
Proteasome subunit beta type-1: 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-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit beta type-10,Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-1

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