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SMTL ID : 6huq.1

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

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:	6 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134, R.135 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 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.175, I:D.178, I:S.181
MG.6:	6 residues within 4Å: Chain K: A.165, H.166, R.167, D.168, A.169 Chain W: D.205 3 PLIP interactions: 1 interactions with chain W, 2 interactions with chain K Metal complexes: W:D.205, K:H.166, K:D.168
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:	4 residues within 4Å: Chain W: A.175, D.178, S.181, D.205 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.178, W:S.181
MG.14:	5 residues within 4Å: Chain I: D.205 Chain Y: A.165, H.166, D.168, A.169 2 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:D.168, I:D.205
MG.15:	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:V.198, Z:D.222

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 GT5: ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-methoxy-1-oxidanylidene-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-2-methyl-1,3-thiazole-5-carboxamide(Covalent)

GT5.3:	16 residues within 4Å: Chain H: T.1, A.20, T.21, E.22, C.31, S.32, K.33, G.45, G.47, A.49, D.53, G.128, S.129 Chain I: D.125, L.126, C.129 13 PLIP interactions: 9 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:T.1, H:E.22, H:K.33, H:A.49, I:D.125, I:L.126 Hydrogen bonds: H:T.21, H:T.21, H:G.47, H:A.49, H:D.53, I:D.125, I:D.125
GT5.5:	16 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, S.130, E.132 13 PLIP interactions: 4 interactions with chain L, 9 interactions with chain K Hydrophobic interactions: L:D.126, L:P.127, K:A.27, K:V.31, K:K.33, K:M.45, K:A.49 Hydrogen bonds: L:D.126, L:S.130, K:T.21, K:T.21, K:G.47, K:A.49
GT5.10:	16 residues within 4Å: Chain V: T.1, A.20, T.21, E.22, C.31, S.32, K.33, G.45, G.47, A.49, D.53, G.128, S.129 Chain W: D.125, L.126, C.129 12 PLIP interactions: 8 interactions with chain V, 4 interactions with chain W Hydrophobic interactions: V:E.22, V:K.33, V:A.49, W:D.125, W:L.126 Hydrogen bonds: V:T.21, V:T.21, V:G.47, V:A.49, V:D.53, W:D.125, W:D.125
GT5.13:	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, S.131 Chain Z: D.126, P.127, S.130, 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:S.130

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 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:T.1, 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 5 PLIP interactions: 5 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:T.1, 1:G.47, 1:S.129, 1: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-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

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-7

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
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Background

Transparent

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Low
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