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SMTL ID : 3mg7.1

Structure of yeast 20S open-gate proteasome with Compound 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 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 F: M.150, A.164, T.165, R.169, K.173 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:A.164
MG.2:	4 residues within 4Å: Chain F: S.13, Y.126, N.127 Chain G: Y.133 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Metal complexes: G:Y.133, F:S.13
MG.3:	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 H: G.162, I.163, D.166, S.169 Chain Z: D.241 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain Z Metal complexes: H:I.163, H:D.166, H:S.169, Z:D.241
MG.5:	2 residues within 4Å: Chain I: G.140, S.143 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:G.140, I:S.143
MG.6:	4 residues within 4Å: Chain I: A.175, D.176, D.178, S.181 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.175, I:D.178, I:S.181
MG.7:	5 residues within 4Å: Chain K: A.165, 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.10:	3 residues within 4Å: Chain D: E.105 Chain L: S.104, S.107 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain D Metal complexes: L:S.104, L:S.107, D:E.105
MG.11:	4 residues within 4Å: Chain L: T.211, H.214, I.215, V.217 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:T.211, L:H.214, L:V.217
MG.12:	6 residues within 4Å: Chain 0: L.67 Chain N: R.19, I.163, D.166, G.167, S.169 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:I.163, N:D.166, N:S.169

2 x L2T: 4-(benzyloxy)-N-[(1S,2R)-2-hydroxy-1-({(1S)-1-[(2-methylbenzyl)carbamoyl]-3-phenylpropyl}carbamoyl)propyl]benzamide(Non-covalent)

L2T.8:

19 residues within 4Å:

Chain K: T.1, R.19, A.20, T.21, V.31, K.33, M.45, A.46, G.47, G.48, A.49, C.52, S.96
Chain L: Y.24, P.123, Y.125, D.145, P.146
Ligands: MES.9

15 PLIP interactions:

8 interactions with chain K, 7 interactions with chain L

Hydrophobic interactions: K:A.20, K:V.31, K:A.49, L:Y.24, L:P.123, L:P.123, L:Y.125, L:P.146
Hydrogen bonds: K:T.1, K:T.21, K:T.21, K:G.47, K:A.49, L:D.145, L:D.145

L2T.13:

20 residues within 4Å:

Chain Y: T.1, R.19, A.20, T.21, A.22, V.31, M.45, A.46, G.47, G.48, A.49, C.52, S.96
Chain Z: Y.24, P.123, Y.125, D.145, P.146, V.147
Ligands: MES.14

14 PLIP interactions:

6 interactions with chain Z, 8 interactions with chain Y

Hydrophobic interactions: Z:Y.24, Z:P.123, Z:Y.125, Z:V.147, Y:A.20, Y:V.31, Y:A.49
Hydrogen bonds: Z:D.145, Z:D.145, Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:A.49

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

MES.9:	6 residues within 4Å: Chain K: T.1, A.46, G.47, G.130, S.131 Ligands: L2T.8 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:S.131
MES.14:	7 residues within 4Å: Chain Y: T.1, A.46, G.47, G.130, S.131, Y.170 Ligands: L2T.13 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:G.47, Y:G.47, Y:S.131

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Blackburn, C. et al., Characterization of a new series of non-covalent proteasome inhibitors with exquisite potency and selectivity for the 20S beta5-subunit. Biochem.J. (2010)

Release Date

2011-05-18

Peptides

Proteasome component Y7: AO
Proteasome component Y13: BP
Proteasome component PRE6: CQ
Proteasome component PUP2: DR
Proteasome component PRE5: ES
Proteasome component C1: FT
Proteasome component C7-alpha: GU
Proteasome component PUP1: HV
Proteasome component PUP3: IW
Proteasome component C11: JX
Proteasome component PRE2: KY
Proteasome component C5: LZ
Proteasome component PRE4: M0
Proteasome component PRE3: 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
1

N
N

1
2

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Proteasome component Y7

Toggle Identical (AO)

Proteasome component Y13

Toggle Identical (BP)

Proteasome component PRE6

Toggle Identical (CQ)

Proteasome component PUP2

Toggle Identical (DR)

Proteasome component PRE5

Toggle Identical (ES)

Proteasome component C1

Toggle Identical (FT)

Proteasome component C7-alpha

Toggle Identical (GU)

Proteasome component PUP1

Toggle Identical (HV)

Proteasome component PUP3

Toggle Identical (IW)

Proteasome component C11

Toggle Identical (JX)

Proteasome component PRE2

Toggle Identical (KY)

Proteasome component C5

Toggle Identical (LZ)

Proteasome component PRE4

Toggle Identical (M0)

Proteasome component PRE3

Toggle Identical (N1)

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Cartoon
Tube
Trace
Lines
Ball+Stick
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Surface
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Fog

Background

Transparent

Resolution

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