SMTL ID : 6hvv.1

Yeast 20S proteasome with human beta2i (1-53) in complex with 39

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

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 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.17, G:R.131, G:M.134 MG.5: 6 residues within 4Å: Chain I: A.175, D.176, D.178, S.181, G.182, D.205 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:A.175, I:S.181 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: 1 interactions with chain W, 2 interactions with chain K Metal complexes: W:D.205, K:A.165, K:D.168 MG.8: 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.11: 6 residues within 4Å: Chain L: D.222 Chain V: 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.13: 5 residues within 4Å: Chain W: A.175, D.178, A.179, S.181, D.205 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.178, W:S.181 MG.15: 5 residues within 4Å: Chain I: D.205 Chain Y: A.165, H.166, D.168, A.169 3 PLIP interactions: 3 interactions with chain Y Metal complexes: Y:A.165, Y:H.166, Y:D.168 MG.16: 6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.192, Z:V.198

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.9: 3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

4 x GT8: (2~{S})-~{N}-[(3~{S},4~{R})-1-cyclohexyl-5-methyl-4,5-bis(oxidanyl)hexan-3-yl]-3-(4-methoxyphenyl)-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide(Covalent)

GT8.3: 18 residues within 4Å: Chain H: T.1, A.20, T.21, N.22, E.32, K.33, G.45, A.46, G.47, V.48, A.49, A.52, E.53, S.129, G.168 Chain I: D.125, L.126 Ligands: MES.4 13 PLIP interactions: 10 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:K.33, H:V.48, H:A.49, H:A.52 Hydrogen bonds: H:T.21, H:T.21, H:G.47, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125 Salt bridges: I:D.125 GT8.6: 18 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, V.31, K.32, K.33, M.45, G.47, G.48, A.49, C.52, Q.53, S.96, S.131, Y.170 Chain L: D.126, V.128 13 PLIP interactions: 11 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:V.31, K:K.33, K:M.45, K:A.49, K:Y.170 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49, L:D.126 Salt bridges: L:D.126 GT8.10: 19 residues within 4Å: Chain V: T.1, A.20, T.21, N.22, E.32, K.33, H.35, G.45, A.46, G.47, V.48, A.49, A.52, E.53, S.129, G.168 Chain W: D.125, L.126 Ligands: MES.12 13 PLIP interactions: 10 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:K.33, V:V.48, V:A.49, V:A.52 Hydrogen bonds: V:T.21, V:T.21, V:G.47, V:G.47, V:G.47, V:A.49, W:D.125, W:D.125 Salt bridges: W:D.125 GT8.14: 18 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, V.31, K.32, K.33, M.45, G.47, G.48, A.49, C.52, Q.53, S.96, S.131, Y.170 Chain Z: D.126, V.128 15 PLIP interactions: 13 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:V.31, Y:K.33, Y:M.45, Y:A.49, Y:Y.170 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:D.126 Water bridges: Y:S.131, Y:S.131 Salt bridges: Z:D.126

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

MES.4: 6 residues within 4Å: Chain H: T.1, G.47, G.128, S.129 Chain Z: Y.33 Ligands: GT8.3 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.129 MES.12: 6 residues within 4Å: Chain L: Y.33 Chain V: T.1, G.47, G.128, S.129 Ligands: GT8.10 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:G.47, V: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-10,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-10,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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