SMTL ID : 5l52.1

Yeast 20S proteasome in complex with epoxyketone inhibitor 14

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

10 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:R.131, G:A.132, G:M.134 MG.3: 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.4: 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.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.7: 2 residues within 4Å: Chain K: T.21 Ligands: 6N5.5 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain L: D.222 Chain V: I.163, W.164, N.165, 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:W.164, V:D.166, L:D.222 MG.11: 5 residues within 4Å: Chain 0: L.47 Chain N: R.19, I.163, D.166, S.169 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:I.163, N:D.166, N:S.169 MG.13: 3 residues within 4Å: Chain X: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain Y: T.21 Ligands: 6N5.14 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain Z: R.28, T.192, H.195, V.198, D.222 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.192, 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.12: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

4 x 6N5: ~{N}-[(2~{S})-1-[[(2~{S})-3-(4-methoxyphenyl)-1-[[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-methyl-5~{H}-indene-2-carboxamide(Covalent)

6N5.5: 19 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, S.131, Y.170 Chain L: D.126, P.127, V.128 Ligands: MG.7, MES.8 14 PLIP interactions: 4 interactions with chain L, 10 interactions with chain K Hydrophobic interactions: L:P.127, L:P.127, L:V.128, K:T.21, K:V.31, K:M.45, K:A.49 Hydrogen bonds: L:D.126, K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49 6N5.10: 16 residues within 4Å: Chain H: H.114, H.116, S.118 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, S.168 15 PLIP interactions: 13 interactions with chain N, 2 interactions with chain H Hydrophobic interactions: N:T.20, N:T.31, N:K.33, 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:S.48, N:S.129, N:S.129, H:S.118 pi-Stacking: H:H.116 6N5.14: 19 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.22, V.31, K.33, M.45, A.46, G.47, G.48, A.49, S.131, Y.170 Chain Z: D.126, P.127, V.128 Ligands: MG.15, MES.16 14 PLIP interactions: 4 interactions with chain Z, 10 interactions with chain Y Hydrophobic interactions: Z:P.127, Z:P.127, Z:V.128, Y:T.21, Y:V.31, Y:M.45, Y:A.49 Hydrogen bonds: Z:D.126, Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49 6N5.18: 16 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, S.168 Chain V: H.114, H.116, S.118 13 PLIP interactions: 11 interactions with chain 1, 2 interactions with chain V 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:S.48, V:S.118 pi-Stacking: V:H.116

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

MES.8: 11 residues within 4Å: Chain J: R.23 Chain K: T.1, G.47, S.96, M.97, G.98, D.116, S.117, G.130, S.131 Ligands: 6N5.5 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:T.1, K:G.47, K:G.47, K:S.131, J:R.23 MES.16: 11 residues within 4Å: Chain X: R.23 Chain Y: T.1, G.47, S.96, M.97, G.98, D.116, S.117, G.130, S.131 Ligands: 6N5.14 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain X Hydrogen bonds: Y:G.47, Y:G.47, Y:S.131, X:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, E.M. et al., A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i. EMBO J. (2016)

Release Date

2016-11-09

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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