SMTL ID : 6e5b.1

Human Immunoproteasome 20S particle in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

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

Ligands

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 2 residues within 4Å: Chain E: R.126, Y.128 No protein-ligand interaction detected (PLIP) SCN.8: 5 residues within 4Å: Chain K: S.99 Chain L: S.151, F.152, S.157, K.164 No protein-ligand interaction detected (PLIP) SCN.16: 2 residues within 4Å: Chain Z: S.151, S.157 No protein-ligand interaction detected (PLIP)

12 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain G: T.14, Y.125, N.128, A.129, M.131 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.128 NA.3: 7 residues within 4Å: Chain H: R.58, I.202, L.203, D.205, L.206, S.208 Chain Z: D.241 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:L.203 NA.4: 4 residues within 4Å: Chain I: V.175, D.178, S.181, D.205 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain Y Hydrogen bonds: I:S.181 Water bridges: Y:R.91 NA.5: 6 residues within 4Å: Chain I: D.205 Chain Y: R.91, T.236, D.239, S.240, S.242 2 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain I Hydrogen bonds: Y:D.239, I:D.205 NA.7: 6 residues within 4Å: Chain K: R.91, T.236, D.239, S.240, S.242 Chain W: D.205 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.240 NA.9: 6 residues within 4Å: Chain L: R.56, A.211, D.214, V.215, T.217, D.241 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.56, L:D.214 NA.10: 7 residues within 4Å: Chain L: D.241 Chain V: R.58, I.202, L.203, D.205, L.206, S.208 2 PLIP interactions: 1 interactions with chain V, 1 interactions with chain L Hydrogen bonds: V:L.203, L:D.241 NA.12: 4 residues within 4Å: Chain N: R.39, M.183, D.186, S.189 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:G.187 NA.13: 5 residues within 4Å: Chain U: T.14, Y.125, N.128, A.129, M.131 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:T.14, U:A.129 NA.14: 4 residues within 4Å: Chain W: V.175, D.178, S.181, D.205 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:D.205 NA.17: 6 residues within 4Å: Chain Z: R.56, A.211, D.214, V.215, T.217, D.241 2 PLIP interactions: 2 interactions with chain Z Hydrogen bonds: Z:R.56, Z:T.217 NA.19: 4 residues within 4Å: Chain 1: R.39, M.183, D.186, S.189 1 PLIP interactions: 1 interactions with chain 1 Hydrogen bonds: 1:S.189

4 x HUJ: [(1R)-3-methyl-1-[[1-[2-[(2,3,4-trimethoxyphenyl)carbonylamino]ethyl]-1,2,3-triazol-4-yl]carbonylamino]butyl]-tris(oxidanyl)boron(Covalent)

HUJ.6: 12 residues within 4Å: Chain K: T.73, R.91, A.92, S.93, G.95, K.105, M.117, S.118, G.119, C.120, A.121, Y.241 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:M.117, K:A.121 Hydrogen bonds: K:T.73, K:S.93, K:S.93, K:G.95, K:G.119, K:G.119, K:G.119, K:A.121 Water bridges: K:A.122 HUJ.11: 10 residues within 4Å: Chain N: T.21, V.40, S.41, G.43, F.51, K.53, L.65, S.66, G.67, A.69 11 PLIP interactions: 11 interactions with chain N Hydrophobic interactions: N:V.40, N:F.51, N:L.65, N:A.69 Hydrogen bonds: N:T.21, N:S.41, N:G.43, N:G.67, N:G.67, N:G.67, N:A.69 HUJ.15: 11 residues within 4Å: Chain Y: T.73, A.92, S.93, A.94, G.95, K.105, M.117, S.118, G.119, A.121, Y.241 10 PLIP interactions: 10 interactions with chain Y Hydrophobic interactions: Y:M.117, Y:A.121 Hydrogen bonds: Y:T.73, Y:S.93, Y:S.93, Y:G.95, Y:G.119, Y:G.119, Y:G.119, Y:A.121 HUJ.18: 10 residues within 4Å: Chain 1: T.21, V.40, S.41, G.43, F.51, K.53, L.65, S.66, G.67, A.69 11 PLIP interactions: 11 interactions with chain 1 Hydrophobic interactions: 1:V.40, 1:F.51, 1:L.65, 1:A.69 Hydrogen bonds: 1:T.21, 1:S.41, 1:G.43, 1:G.67, 1:G.67, 1:G.67, 1:A.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ladi, E. et al., Design and Evaluation of Highly Selective Human Immunoproteasome Inhibitors Reveal a Compensatory Process That Preserves Immune Cell Viability. J.Med.Chem. (2019)

Release Date

2019-09-11

Peptides

Proteasome subunit alpha type-2: AO
Proteasome subunit alpha type-4: BP
Proteasome subunit alpha type-7: CQ
Proteasome subunit alpha type-5: DR
Proteasome subunit alpha type-1: ES
Proteasome subunit alpha type-3: FT
Proteasome subunit alpha type-6: GU
Proteasome subunit beta type-10: HV
Proteasome subunit beta type-3: IW
Proteasome subunit beta type-2: JX
Proteasome subunit beta type-8: KY
Proteasome subunit beta type-1: LZ
Proteasome subunit beta type-4: M0
Proteasome subunit beta type-9: 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-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-5

Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit alpha type-6

Proteasome subunit beta type-10

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-8

Proteasome subunit beta type-1

Proteasome subunit beta type-4

Proteasome subunit beta type-9

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