SMTL ID : 5m2b.1

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with thiazole based inhibitor Ro19

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

7 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.3: 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.4: 3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.6: 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.7: 7 residues within 4Å: Chain L: D.222 Chain V: R.19, G.162, I.163, D.166, L.167, S.169 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, V:S.169, L:D.222 MG.8: 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.12: 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

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.9: 3 residues within 4Å: Chain N: T.31, R.45, Q.53 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain 1: T.31, R.45, Q.53 Ligand excluded by PLIP

2 x 7DX: (2~{S})-2-cyclohexyl-4-oxidanylidene-4-[[7-(4-phenyl-1,3-thiazol-2-yl)quinolin-2-yl]amino]butanoic acid(Non-covalent)

7DX.5: 17 residues within 4Å: Chain K: T.1, V.31, N.32, K.33, M.45, S.46, G.47, A.49, Q.53, G.129, S.130 Chain L: S.124, F.125, D.126, Y.131, Q.132, R.137 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:V.31, K:V.31, K:K.33, K:A.49 Hydrogen bonds: K:T.1, K:G.47, K:S.130 7DX.11: 16 residues within 4Å: Chain Y: T.1, V.31, K.33, M.45, S.46, G.47, A.49, Q.53, G.129, S.130 Chain Z: S.124, F.125, D.126, Y.131, Q.132, R.137 7 PLIP interactions: 7 interactions with chain Y Hydrophobic interactions: Y:V.31, Y:A.49 Hydrogen bonds: Y:T.1, Y:T.1, Y:G.47, Y:S.130 pi-Cation interactions: Y:K.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, H. et al., Structural Elucidation of a Nonpeptidic Inhibitor Specific for the Human Immunoproteasome. Chembiochem (2017)

Release Date

2017-01-25

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

Proteasome subunit beta type-7

Proteasome subunit beta type-1

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