SMTL ID : 6htd.1

Yeast 20S proteasome with human beta2c (S171G) in complex with 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain K: R.19, A.165, H.166, D.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:D.168, K:S.171, W:D.205 MG.7: 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, F.164, 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:F.164, V:D.166, L:D.222 MG.12: 5 residues within 4Å: Chain W: A.175, D.176, D.178, S.181, D.205 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:A.175, W:D.178 MG.14: 5 residues within 4Å: Chain I: D.205 Chain Y: A.165, H.166, D.168, A.169 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain Y Metal complexes: I:D.205, Y:H.166, Y:D.168 MG.15: 6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 1 PLIP interactions: 1 interactions with chain Z Metal complexes: 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.9: 2 residues within 4Å: Chain U: R.120, N.123 Ligand excluded by PLIP

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

GQH.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, G.47, T.48, A.49, D.53, G.128, S.129 Chain I: D.125, L.126, C.129, D.131 15 PLIP interactions: 11 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:A.20, H:E.22, H:A.27, H:K.33, H:T.48, H:A.49, I:L.126, I:D.131 Hydrogen bonds: H:T.21, H:T.21, H:S.32, H:G.47, H:A.49, I:D.125, I:D.125 GQH.5: 15 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, S.131 Chain L: D.126, P.127, E.132 12 PLIP interactions: 9 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:A.27, K:V.31, K:K.33, K:M.45, K:A.49, L:P.127 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:A.49, L:D.126, L:E.132 GQH.10: 18 residues within 4Å: Chain V: T.1, A.20, T.21, E.22, A.27, C.31, S.32, K.33, G.45, G.47, T.48, A.49, D.53, G.128, S.129 Chain W: D.125, L.126, C.129 15 PLIP interactions: 12 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:A.20, V:E.22, V:A.27, V:K.33, V:T.48, V:A.49, W:L.126 Hydrogen bonds: V:T.21, V:T.21, V:E.22, V:S.32, V:G.47, V:A.49, W:D.125, W:D.125 GQH.13: 16 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 Chain Z: D.126, P.127, E.132 12 PLIP interactions: 9 interactions with chain Y, 3 interactions with chain Z Hydrophobic interactions: Y:A.27, Y:V.31, Y:K.33, Y:M.45, Y:A.49, Z:P.127 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:A.49, Z:D.126, Z:E.132

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

SO4.8: 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 6 PLIP interactions: 6 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:T.1, 1:G.47, 1:S.129, 1:S.129 Water bridges: 1:G.128

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

Related Entries With Identical Sequence