9ey9.1 | SWISS-MODEL Template Library

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SMTL ID : 9ey9.1

Yeast 20S proteasome in complex with a sybactin derivative (PheSyr)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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:	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:	3 residues within 4Å: Chain H: Q.90 Chain N: D.51, N.92 No protein-ligand interaction detected (PLIP)
MG.4:	4 residues within 4Å: Chain I: A.175, D.178, S.181, D.205 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.181
MG.6:	7 residues within 4Å: Chain K: R.18, A.164, H.165, D.167, A.168, S.170 Chain W: D.205 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.164, K:D.167, K:S.170, W:D.205
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.9:	8 residues within 4Å: Chain L: D.222 Chain V: G.161, I.162, W.163, N.164, D.165, L.166, S.168 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.162, V:D.165, L:D.222
MG.11:	7 residues within 4Å: Chain I: D.205 Chain Y: R.18, A.164, H.165, D.167, A.168, S.170 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.164, Y:D.167, I:D.205
MG.12:	7 residues within 4Å: Chain H: R.18 Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:V.198

4 x 01: sybactin derivative

01.2:	20 residues within 4Å: Chain H: T.1, I.2, D.16, S.19, T.20, C.30, K.32, G.44, A.45, G.46, T.47, A.48, T.51, L.126, G.127, S.128, G.129, G.167, S.168 Chain I: D.125 18 PLIP interactions: 3 interactions with chain I, 15 interactions with chain H Hydrophobic interactions: I:D.125, H:I.2, H:K.32, H:A.45, H:T.47, H:A.48 Hydrogen bonds: I:D.125, I:D.125, H:T.1, H:T.20, H:T.20, H:K.32, H:G.46, H:G.46, H:A.48, H:S.128, H:S.128, H:G.129
01.5:	18 residues within 4Å: Chain K: T.1, D.16, A.19, T.20, V.30, K.32, G.46, A.48, G.129, S.130, G.131, D.167, Y.169, S.170 Chain L: D.126, P.127, V.128, S.130 17 PLIP interactions: 12 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: K:A.19, K:V.30, K:A.48, L:D.126, L:P.127, L:V.128 Hydrogen bonds: K:T.20, K:T.20, K:K.32, K:G.46, K:G.46, K:A.48, K:S.130, K:S.130, K:G.131, L:D.126, L:S.130
01.8:	21 residues within 4Å: Chain V: T.1, I.2, D.16, S.19, T.20, C.30, K.32, A.45, G.46, T.47, A.48, L.126, G.127, S.128, G.129, D.165, G.167, S.168 Chain W: D.125, L.126, C.129 18 PLIP interactions: 14 interactions with chain V, 4 interactions with chain W Hydrophobic interactions: V:I.2, V:K.32, V:A.45, V:A.48, W:D.125, W:L.126 Hydrogen bonds: V:S.19, V:T.20, V:T.20, V:K.32, V:G.46, V:G.46, V:A.48, V:S.128, V:S.128, V:G.129, W:D.125, W:D.125
01.10:	17 residues within 4Å: Chain Y: T.1, D.16, R.18, A.19, T.20, V.30, K.32, G.46, A.48, G.129, S.130, G.131, D.167, Y.169, S.170 Chain Z: D.126, V.128 15 PLIP interactions: 12 interactions with chain Y, 3 interactions with chain Z Hydrophobic interactions: Y:A.19, Y:V.30, Y:A.48, Z:D.126, Z:V.128 Hydrogen bonds: Y:T.20, Y:T.20, Y:K.32, Y:G.46, Y:G.46, Y:A.48, Y:S.130, Y:S.130, Y:G.131, Z:D.126

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Prave, L. et al., Bioengineering of syrbactin megasynthetases for immunoproteasome inhibitor production. Chem (2024)

Release Date

2025-02-19

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 endopeptidase complex: HV
Proteasome subunit beta type-3: IW
Proteasome subunit beta type-4: JX
proteasome endopeptidase complex: 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 endopeptidase complex

Toggle Identical (HV)

Proteasome subunit beta type-3

Toggle Identical (IW)

Proteasome subunit beta type-4

Toggle Identical (JX)

proteasome endopeptidase complex

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
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Background

Transparent

Resolution

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