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SMTL ID : 4jsu.1

Yeast 20S proteasome in complex with the dimerized linear mimetic of TMC-95A - yCP:3a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

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

Ligands

4 x ACA- TY5- ALA- RE0- ABN: TMC-95A mimic ligand yCP:3a(Non-covalent)

ACA-TY5-ALA-RE0-ABN.1:	17 residues within 4Å: Chain K: T.1, A.20, T.21, A.22, G.23, V.31, K.33, M.45, G.47, G.48, A.49 Chain L: F.102, P.104, Y.106, D.126, V.128 Ligands: MES.5 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:A.20, K:V.31, K:M.45, K:A.49, L:P.104, L:V.128, L:V.128 Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:G.23, K:G.47, K:A.49, L:D.126
ACA-TY5-ALA-RE0-ABN.2:	18 residues within 4Å: Chain Y: T.1, A.20, T.21, A.22, G.23, V.31, K.33, M.45, G.47, G.48, A.49 Chain Z: F.102, P.104, Y.106, D.126, P.127, V.128 Ligands: MES.6 14 PLIP interactions: 4 interactions with chain Z, 10 interactions with chain Y Hydrophobic interactions: Z:P.104, Z:V.128, Z:V.128, Y:A.20, Y:V.31, Y:M.45, Y:A.49 Hydrogen bonds: Z:D.126, Y:T.1, Y:T.21, Y:T.21, Y:G.23, Y:G.47, Y:A.49
ACA-TY5-ALA-RE0-ABN.3:	19 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, C.31, A.32, K.33, G.45, G.47, T.48, A.49, T.52 Chain I: R.99, F.100, P.102, D.125, L.126, I.127 Chain Z: Y.33 17 PLIP interactions: 8 interactions with chain I, 1 interactions with chain Z, 8 interactions with chain H Hydrophobic interactions: I:L.126, I:I.127, I:I.127, Z:Y.33, H:K.33, H:A.49 Hydrogen bonds: I:R.99, I:D.125, I:D.125, H:T.21, H:T.21, H:T.21, H:T.21, H:G.47, H:A.49 Water bridges: I:L.126 pi-Cation interactions: I:R.99
ACA-TY5-ALA-RE0-ABN.4:	17 residues within 4Å: Chain L: Y.33 Chain V: T.1, S.20, T.21, C.31, A.32, K.33, G.45, G.47, T.48, A.49 Chain W: R.99, F.100, P.102, D.125, L.126, I.127 17 PLIP interactions: 8 interactions with chain V, 1 interactions with chain L, 8 interactions with chain W Hydrophobic interactions: V:K.33, V:A.49, L:Y.33, W:L.126, W:I.127, W:I.127 Hydrogen bonds: V:T.21, V:T.21, V:T.21, V:T.21, V:G.47, V:A.49, W:R.99, W:D.125, W:D.125 Water bridges: W:L.126 pi-Cation interactions: W:R.99

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

MES.5:	9 residues within 4Å: Chain K: T.1, T.21, A.46, G.47, G.130, S.131, Y.170 Ligands: ACA-TY5-ALA-RE0-ABN.1, ACA-TY5-ALA-RE0-ABN.1 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:S.131
MES.6:	9 residues within 4Å: Chain Y: T.1, T.21, A.46, G.47, G.130, S.131, Y.170 Ligands: ACA-TY5-ALA-RE0-ABN.2, ACA-TY5-ALA-RE0-ABN.2 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:T.1, Y:G.47, Y:S.131

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Desvergne, A. et al., Dimerized linear mimics of a natural cyclopeptide (TMC-95A) are potent noncovalent inhibitors of the eukaryotic 20S proteasome. J.Med.Chem. (2013)

Release Date

2013-05-01

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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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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