SMTL ID : 5d0t.1

Yeast 20S proteasome beta5-D166N mutant in complex with MG132

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

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

Ligands

11 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.17, G:R.131, G:M.134 MG.3: 6 residues within 4Å: Chain I: A.175, D.178, A.179, S.181, D.205 Chain Y: R.19 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.178, I:S.181 MG.4: 7 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, N.168, A.169, S.171 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:N.168, I:D.205 MG.5: 3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.7: 7 residues within 4Å: Chain K: R.19, A.165, H.166, N.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:N.168, K:S.171, W:D.205 MG.8: 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: 1 interactions with chain L, 3 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166, V:S.169 MG.9: 4 residues within 4Å: Chain M: T.22, S.23, L.197, D.201 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:S.23, M:D.201 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.14: 3 residues within 4Å: Chain X: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.16: 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 MG.18: 5 residues within 4Å: Chain 1: T.1, G.47, G.128, S.129 Ligands: ALD.17 No protein-ligand interaction detected (PLIP)

4 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: 5 residues within 4Å: Chain N: T.31, R.45, A.49, Q.53 Ligands: ALD.10 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain 1: T.31, R.45, A.49, Q.53 Chain V: D.120 Ligands: ALD.17 Ligand excluded by PLIP

4 x ALD: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide(Covalent)

ALD.6: 13 residues within 4Å: Chain K: T.1, A.20, T.21, A.27, V.31, K.33, M.45, A.46, G.47, A.49 Chain L: D.126, P.127, S.130 13 PLIP interactions: 11 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:A.20, K:A.27, K:V.31, K:M.45, K:A.49, L:P.127 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49, L:D.126 ALD.10: 15 residues within 4Å: Chain H: H.114, H.116, S.118, D.120 Chain N: T.1, T.20, T.21, T.22, K.33, R.45, G.47, S.48, A.49, T.52 Ligands: CL.12 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:T.20 Hydrogen bonds: N:T.1, N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49 pi-Stacking: H:H.116 ALD.15: 13 residues within 4Å: Chain Y: T.1, A.20, T.21, A.27, V.31, K.33, M.45, A.46, G.47, A.49 Chain Z: D.126, P.127, S.130 13 PLIP interactions: 11 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.20, Y:A.27, Y:V.31, Y:M.45, Y:A.49, Z:P.127 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:D.126 ALD.17: 16 residues within 4Å: Chain 1: T.1, T.20, T.21, T.22, K.33, R.45, G.47, S.48, A.49, T.52 Chain V: H.114, H.116, S.118, D.120 Ligands: MG.18, CL.19 10 PLIP interactions: 7 interactions with chain 1, 3 interactions with chain V Hydrophobic interactions: 1:T.20 Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:A.49 Water bridges: V:S.118, V:S.118 pi-Stacking: V:H.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, E.M. et al., A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Nat Commun (2016)

Release Date

2016-03-23

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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