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SMTL ID : 6h39.1

Yeast 20S proteasome in complex with the peptidic non-covalent binding inhibitor RTS-V5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

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

Ligands

10 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:	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.5:	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: 1 interactions with chain W, 3 interactions with chain K Metal complexes: W:D.205, K:A.165, K:D.168, K:S.171
MG.6:	5 residues within 4Å: Chain K: T.1, T.21, Y.170 Ligands: FGY.4, MES.7 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.21
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.11:	7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.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:D.166, V:S.169, L:D.222
MG.12:	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:	3 residues within 4Å: Chain Y: T.21, G.23 Ligands: MES.16 2 PLIP interactions: 2 interactions with chain Y Metal complexes: Y:T.21, Y:G.23
MG.17:	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.10:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

2 x FGY: N-(2,2-dimethylpropyl)-N~2~-[4-(hydroxycarbamoyl)benzene-1-carbonyl]-L-asparaginyl-N-benzyl-L-alaninamide(Non-covalent)

FGY.4:

22 residues within 4Å:

Chain K: T.1, A.20, T.21, A.22, A.27, S.28, V.31, K.33, M.45, G.47, A.49
Chain L: Y.106, S.124, D.126, P.127, V.128, S.130, Y.131, E.132, R.137
Ligands: MG.6, MES.7

15 PLIP interactions:

9 interactions with chain K, 6 interactions with chain L

Hydrophobic interactions: K:V.31, K:M.45, K:A.49, L:P.127, L:V.128, L:E.132
Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:G.47, K:A.49, L:D.126, L:S.130, L:S.130
Water bridges: K:A.50

FGY.13:

17 residues within 4Å:

Chain Y: T.1, A.20, T.21, A.22, V.31, K.33, M.45, G.47, A.49
Chain Z: S.124, F.125, D.126, P.127, V.128, S.130, R.137
Ligands: MES.16

13 PLIP interactions:

5 interactions with chain Z, 8 interactions with chain Y

Hydrophobic interactions: Z:D.126, Z:P.127, Z:V.128, Y:A.20, Y:V.31, Y:M.45, Y:A.49
Hydrogen bonds: Z:D.126, Z:S.130, Y:T.21, Y:T.21, Y:G.47, Y:A.49

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

MES.7:	7 residues within 4Å: Chain K: T.1, G.47, G.130, S.131, Y.170 Ligands: FGY.4, MG.6 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:S.131 Water bridges: K:S.96
MES.16:	7 residues within 4Å: Chain Y: T.1, G.47, G.130, S.131, Y.170 Ligands: FGY.13, MG.15 4 PLIP interactions: 4 interactions with chain Y Hydrogen bonds: Y:T.1, Y:G.47, Y:G.47, Y:S.131

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

SO4.9:	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
SO4.18:	5 residues within 4Å: Chain 1: T.1, S.46, G.47, G.128, S.129 7 PLIP interactions: 7 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:T.1, 1:G.47, 1:G.47, 1:S.129, 1:S.129 Water bridges: 1:G.128

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bhatia, S. et al., Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. J. Med. Chem. (2018)

Release Date

2018-11-07

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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