SMTL ID : 6g8m.1

Yeast 20S proteasome in complex with Cystargolide B Derivative 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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.4: 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.19, A.165, H.166, D.168, A.169, S.171 Chain W: D.205 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.165, K:D.168, K:S.171, W:D.205 MG.8: 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.11: 7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, D.166, L.167, S.169 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, V:S.169, L:D.222 MG.12: 5 residues within 4Å: Chain W: A.175, D.178, A.179, S.181, D.205 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.178, W:S.181 MG.14: 7 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, D.168, A.169, S.171 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:D.168, Y:S.171, I:D.205 MG.15: 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

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

CL.2: 3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

6 x EQE: (2~{S},3~{R})-4-[[(2~{S})-3-methyl-1-[[(2~{S})-3-methyl-1-oxidanylidene-1-phenylmethoxy-butan-2-yl]amino]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanyl-4-oxidanylidene-2-propan-2-yl-butanoic acid(Covalent)

EQE.3: 15 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, K.33, G.45, A.46, G.47, A.49, Y.97, G.128, S.129, S.131 Chain N: Y.25 Chain Z: Y.33 12 PLIP interactions: 10 interactions with chain H, 1 interactions with chain N, 1 interactions with chain Z Hydrophobic interactions: H:K.33, H:A.46, H:A.49, H:Y.97, N:Y.25, Z:Y.33 Hydrogen bonds: H:T.1, H:T.1, H:R.19, H:K.33, H:G.47, H:S.129 EQE.5: 11 residues within 4Å: Chain K: T.1, R.19, T.21, K.33, M.45, A.46, G.47, G.130, S.131, Y.170 Chain W: S.33 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:Y.170 Hydrogen bonds: K:T.1, K:T.1, K:R.19, K:G.47, K:S.131 EQE.7: 13 residues within 4Å: Chain H: Y.97, H.114, S.118 Chain N: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49 9 PLIP interactions: 2 interactions with chain H, 7 interactions with chain N Hydrophobic interactions: H:Y.97, N:T.22, N:A.49 Salt bridges: H:H.114 Hydrogen bonds: N:T.21, N:T.21, N:G.47, N:G.47, N:A.49 EQE.10: 16 residues within 4Å: Chain 1: Y.25 Chain L: Y.33 Chain V: T.1, R.19, S.20, T.21, K.33, G.45, A.46, G.47, A.49, Y.97, G.128, S.129, S.131, L.132 12 PLIP interactions: 10 interactions with chain V, 1 interactions with chain L, 1 interactions with chain 1 Hydrophobic interactions: V:A.46, V:A.49, V:Y.97, V:L.132, L:Y.33, 1:Y.25 Hydrogen bonds: V:T.1, V:T.1, V:R.19, V:K.33, V:G.47, V:S.129 EQE.13: 11 residues within 4Å: Chain I: S.33 Chain Y: T.1, R.19, T.21, K.33, M.45, A.46, G.47, G.130, S.131, Y.170 8 PLIP interactions: 8 interactions with chain Y Hydrophobic interactions: Y:Y.170 Hydrogen bonds: Y:T.1, Y:T.1, Y:R.19, Y:K.33, Y:G.47, Y:S.131 Water bridges: Y:T.21 EQE.16: 12 residues within 4Å: Chain 1: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49 Chain V: H.114, S.118 9 PLIP interactions: 7 interactions with chain 1, 2 interactions with chain V Hydrophobic interactions: 1:T.20, 1:T.22, 1:A.49 Hydrogen bonds: 1:T.21, 1:T.21, 1:G.47, 1:A.49, V:S.118 Salt bridges: V:H.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niroula, D. et al., Design, synthesis, and evaluation of cystargolide-based beta-lactones as potent proteasome inhibitors. Eur J Med Chem (2018)

Release Date

2018-09-12

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-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-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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