SMTL ID : 6hub.1

Yeast 20S proteasome with human beta2c (S171G) in complex with 16

Coordinates

PDB Format

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.4: 5 residues within 4Å: Chain I: A.175, D.176, 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.5: 5 residues within 4Å: Chain I: D.205 Chain Y: A.165, H.166, D.168, A.169 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:H.166, Y:D.168, I:D.205 MG.7: 6 residues within 4Å: Chain K: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.165, K:D.168, W:D.205 MG.8: 6 residues within 4Å: Chain L: D.222 Chain V: I.163, F.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.9: 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.13: 5 residues within 4Å: Chain W: A.175, D.176, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:A.175, W:D.178, W:S.181 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: 2 residues within 4Å: Chain G: R.120, N.123 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain U: R.120, N.123 Ligand excluded by PLIP

4 x GRW: (2~{S})-~{N}-[(2~{S},3~{R})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2-[[(2~{R})-2-azido-3-phenyl-propanoyl]amino]-4-methyl-pentanamide(Covalent)

GRW.3: 19 residues within 4Å: Chain H: T.1, A.20, T.21, E.22, A.27, C.31, S.32, K.33, G.45, A.46, G.47, T.48, A.49, D.53, G.128, S.129 Chain I: D.125, L.126, C.129 15 PLIP interactions: 12 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:E.22, H:A.27, H:K.33, H:T.48, H:A.49, I:L.126 Hydrogen bonds: H:T.21, H:T.21, H:T.21, H:T.21, H:H.35, H:G.47, H:A.49, I:D.125, I:D.125 GRW.6: 19 residues within 4Å: Chain K: T.1, A.20, T.21, A.27, V.31, K.32, K.33, M.45, G.47, A.49, Q.53, G.130, S.131, Y.170 Chain L: P.104, D.126, P.127, S.130, E.132 15 PLIP interactions: 10 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: K:A.27, K:V.31, K:K.33, K:M.45, K:A.49, L:P.104, L:D.126, L:P.127 Hydrogen bonds: K:T.21, K:T.21, K:T.21, K:G.47, K:A.49, L:D.126, L:S.130 GRW.12: 18 residues within 4Å: Chain V: T.1, A.20, T.21, E.22, C.31, S.32, K.33, G.45, A.46, G.47, T.48, A.49, D.53, G.128, S.129 Chain W: D.125, L.126, C.129 13 PLIP interactions: 10 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:T.1, V:T.48, V:A.49, W:D.125 Hydrogen bonds: V:T.21, V:T.21, V:T.21, V:T.21, V:E.22, V:G.47, V:A.49, W:D.125, W:D.125 GRW.14: 19 residues within 4Å: Chain Y: T.1, A.20, T.21, A.27, V.31, K.32, K.33, M.45, G.47, A.49, Q.53, G.130, S.131, Y.170 Chain Z: P.104, D.126, P.127, S.130, E.132 15 PLIP interactions: 5 interactions with chain Z, 10 interactions with chain Y Hydrophobic interactions: Z:P.104, Z:D.126, Z:P.127, Y:A.27, Y:V.31, Y:K.33, Y:M.45, Y:A.49 Hydrogen bonds: Z:D.126, Z:S.130, Y:T.21, Y:T.21, Y:T.21, Y:G.47, Y:A.49

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 5 residues within 4Å: Chain N: T.1, S.46, G.47, G.128, S.129 5 PLIP interactions: 5 interactions with chain N Hydrogen bonds: N:T.1, N:G.47, N:G.47, N:S.129, N:S.129 SO4.16: 5 residues within 4Å: Chain 1: T.1, S.46, G.47, G.128, S.129 5 PLIP interactions: 5 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:T.1, 1:G.47, 1:S.129, 1:S.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xin, B.T. et al., Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits. J.Med.Chem. (2019)

Release Date

2019-01-30

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-7: 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-7

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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