SMTL ID : 5l5j.1

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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: 6 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.164, 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.7: 3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain K: R.19, 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: 6 residues within 4Å: Chain L: D.222 Chain V: I.163, W.164, D.166, L.167, S.169 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166 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.16: 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.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)

6N5.3: 19 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain I: D.125, L.126, I.127 Ligands: MES.4 13 PLIP interactions: 9 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:K.33, H:A.49, I:L.126, I:I.127 Hydrogen bonds: H:T.21, H:T.21, H:Q.22, H:G.47, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125 6N5.8: 18 residues within 4Å: Chain K: T.1, R.19, A.20, S.21, A.22, V.31, K.33, M.45, S.46, G.47, C.48, A.49, S.130, Y.169 Chain L: Y.108, D.126, P.127, V.128 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:V.31, K:K.33, K:M.45, K:A.49, L:P.127, L:V.128 Hydrogen bonds: K:S.21, K:S.21, K:G.47, K:G.47, K:G.47, K:A.49, L:Y.108, L:D.126 6N5.13: 18 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain W: D.125, L.126, I.127 14 PLIP interactions: 4 interactions with chain W, 10 interactions with chain V Hydrophobic interactions: W:L.126, W:I.127, V:K.33, V:A.49 Hydrogen bonds: W:D.125, W:D.125, V:T.21, V:T.21, V:Q.22, V:G.47, V:G.47, V:G.47, V:A.49 Water bridges: V:S.129 6N5.14: 18 residues within 4Å: Chain Y: T.1, R.19, A.20, S.21, A.22, K.33, M.45, S.46, G.47, C.48, A.49, S.130, Y.169 Chain Z: Y.108, D.126, P.127, V.128 Ligands: MES.15 14 PLIP interactions: 4 interactions with chain Z, 10 interactions with chain Y Hydrophobic interactions: Z:P.127, Z:V.128, Y:K.33, Y:M.45, Y:A.49 Hydrogen bonds: Z:Y.108, Z:D.126, Y:S.21, Y:S.21, Y:S.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49

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

MES.4: 6 residues within 4Å: Chain H: A.46, G.47, Y.97, G.128, S.129 Ligands: 6N5.3 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:G.47, H:G.128, H:S.129 pi-Cation interactions: H:Y.97 MES.15: 4 residues within 4Å: Chain Y: G.47, G.129, S.130 Ligands: 6N5.14 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:G.47, Y:S.130

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-8,Proteasome subunit beta type-5: KY
Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,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-8,Proteasome subunit beta type-5

Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6,Proteasome subunit beta type-1,Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-1

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