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SMTL ID : 8rhl.1

Yeast 20S proteasome in complex with a linear biarylether epoxyketone (compound 15a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

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

Ligands

4 x ACE- PPN- LEU- TYR- 6VO: Linear biarylether epoxyketone(Non-covalent)

ACE-PPN-LEU-TYR-6VO.1:	14 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, A.27, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain I: D.125 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:Q.22, H:A.27, H:A.49 Hydrogen bonds: H:T.21, H:T.21, H:Q.22, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125 Water bridges: H:S.129, H:S.129
ACE-PPN-LEU-TYR-6VO.2:	17 residues within 4Å: Chain K: T.1, A.20, T.21, A.22, A.27, K.33, A.46, G.47, G.48, A.49, G.94, S.131, Y.170 Chain L: D.126, P.127, V.128 Ligands: MES.8 13 PLIP interactions: 11 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:A.20, K:A.22, K:A.27, K:A.49, L:D.126 Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49, L:D.126
ACE-PPN-LEU-TYR-6VO.3:	14 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, A.27, K.33, G.45, A.46, G.47, T.48, A.49, S.129, G.168 Chain W: D.125 16 PLIP interactions: 13 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:Q.22, V:A.27, V:K.33, V:A.49, W:D.125 Hydrogen bonds: V:T.21, V:T.21, V:Q.22, V:G.47, V:G.47, V:G.47, V:A.49, W:D.125, W:D.125 Water bridges: V:S.129, V:S.129
ACE-PPN-LEU-TYR-6VO.4:	15 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.22, A.27, K.33, G.47, G.48, A.49, S.131, Y.170 Chain Z: D.126, P.127, V.128 13 PLIP interactions: 2 interactions with chain Z, 11 interactions with chain Y Hydrophobic interactions: Z:D.126, Y:A.20, Y:A.22, Y:A.49 Hydrogen bonds: Z:D.126, Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49 Water bridges: Y:S.131, Y:S.131

8 x MG: MAGNESIUM ION(Non-covalent)

MG.5:	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:R.131, G:A.132, G:M.134
MG.7:	4 residues within 4Å: Chain I: A.175, 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.9:	7 residues within 4Å: Chain K: R.19, 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.10:	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.12:	6 residues within 4Å: Chain L: D.222 Chain V: I.163, W.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.13:	3 residues within 4Å: Chain X: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP)
MG.14:	7 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, D.168, A.169, S.171 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:D.168, Y:S.171, I:D.205
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.6:	3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP
CL.11:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

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

MES.8:

6 residues within 4Å:

Chain K: T.1, G.47, G.130, S.131, Y.170
Ligands: ACE-PPN-LEU-TYR-6VO.2

2 PLIP interactions:

2 interactions with chain K

Hydrogen bonds: K:G.47, K:S.131

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Gotz, M.G. et al., Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome. Acs Med.Chem.Lett. (2024)

Release Date

2024-05-01

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-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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Proteasome subunit alpha type-2

Toggle Identical (AO)

Proteasome subunit alpha type-3

Toggle Identical (BP)

Proteasome subunit alpha type-4

Toggle Identical (CQ)

Proteasome subunit alpha type-5

Toggle Identical (DR)

Proteasome subunit alpha type-6

Toggle Identical (ES)

Probable proteasome subunit alpha type-7

Toggle Identical (FT)

Proteasome subunit alpha type-1

Toggle Identical (GU)

Proteasome subunit beta type-2

Toggle Identical (HV)

Proteasome subunit beta type-3

Toggle Identical (IW)

Proteasome subunit beta type-4

Toggle Identical (JX)

Proteasome subunit beta type-5

Toggle Identical (KY)

Proteasome subunit beta type-6

Toggle Identical (LZ)

Proteasome subunit beta type-7

Toggle Identical (M0)

Proteasome subunit beta type-1

Toggle Identical (N1)

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Background

Transparent

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