SMTL ID : 5l5o.1

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 16

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-oligomer

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: 6 residues within 4Å: Chain K: R.19, A.164, 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: 7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, D.166, L.167, S.169 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, 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.16: 4 residues within 4Å: Chain Z: T.192, H.195, I.196, V.198 4 PLIP interactions: 3 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: Z:T.192, Z:H.195, Z:V.198, H2O.17

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 79P: (2~{S})-3-(1~{H}-indol-3-yl)-~{N}-[(2~{S},3~{S},4~{R})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]-2-[[(2~{R})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide(Covalent)

79P.3: 16 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, G.168 Chain I: D.125 Ligands: MES.4 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:Q.22, H:K.33, H:A.49 Hydrogen bonds: H:T.21, H:T.21, H:G.47, H:G.47, H:G.47, H:A.49, I:D.125 79P.8: 18 residues within 4Å: Chain K: T.1, R.19, A.20, S.21, S.27, V.31, K.33, M.45, S.46, G.47, C.48, A.49, S.96, Y.169 Chain L: S.124, D.126, S.130, Q.132 15 PLIP interactions: 12 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:V.31, K:K.33, K:M.45, K:A.49 Hydrogen bonds: K:S.21, K:S.21, K:S.27, K:G.47, K:G.47, K:G.47, K:A.49, L:D.126, L:S.130 Water bridges: K:S.130 Salt bridges: L:D.126 79P.13: 17 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, I.127 13 PLIP interactions: 2 interactions with chain W, 11 interactions with chain V Hydrogen bonds: W:D.125, W:D.125, V:T.21, V:T.21, V:G.47, V:G.47, V:G.47, V:A.49 Hydrophobic interactions: V:Q.22, V:K.33, V:A.49 Water bridges: V:S.129, V:S.129 79P.14: 20 residues within 4Å: Chain Y: T.1, R.19, A.20, S.21, S.27, V.31, K.33, M.45, S.46, G.47, C.48, A.49, S.96, Y.169 Chain Z: Y.108, S.124, D.126, S.130, Q.132 Ligands: MES.15 14 PLIP interactions: 11 interactions with chain Y, 3 interactions with chain Z Hydrophobic interactions: Y:K.33, Y:M.45, Y:A.49 Hydrogen bonds: Y:S.21, Y:S.21, Y:S.21, Y:S.27, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:D.126, Z:S.130 Salt bridges: Z:D.126

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

MES.4: 7 residues within 4Å: Chain H: A.46, G.47, Y.97, H.114, G.128, S.129 Ligands: 79P.3 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.47, H:S.129 MES.15: 4 residues within 4Å: Chain Y: G.47, G.129, S.130 Ligands: 79P.14 2 PLIP interactions: 2 interactions with chain Y Hydrogen bonds: Y:S.130 Water bridges: Y:G.129

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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