7o2l.1 | SWISS-MODEL Template Library

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SMTL ID : 7o2l.1

Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)

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 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.17, G:R.131, G:M.134
MG.4:	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.6:	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: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.165, K:D.168, K:S.171, W:D.205
MG.8:	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, W.164, D.166, L.167, S.169 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, L:D.222
MG.12:	5 residues within 4Å: Chain W: A.175, D.176, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:A.175, W:D.178, W:S.181
MG.14:	7 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, D.168, A.169, S.171 3 PLIP interactions: 2 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:D.168, I:D.205
MG.15:	5 residues within 4Å: Chain Z: R.28, T.192, H.195, V.198, D.222 2 PLIP interactions: 1 interactions with chain Z, 1 Ligand-Water interactions Metal complexes: Z:V.198, H₂O.5

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.9:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

6 x V08: (2 {R},3 {S})-3-methanoyl-4-methyl-2-hydroxy-pentanoic acid(Covalent)

V08.3:	4 residues within 4Å: Chain H: T.1, A.46, G.47, G.168 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:T.1, H:G.47
V08.5:	9 residues within 4Å: Chain K: T.1, R.19, A.20, K.33, M.45, A.46, G.47, S.131, Y.170 6 PLIP interactions: 6 interactions with chain K Hydrogen bonds: K:T.1, K:T.21, K:K.33, K:G.47 Water bridges: K:S.131, K:S.131
V08.7:	5 residues within 4Å: Chain N: T.1, R.45, S.46, G.47, S.168 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:T.1, N:G.47
V08.10:	7 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, A.46, G.47, G.168 3 PLIP interactions: 3 interactions with chain V Hydrogen bonds: V:T.1, V:R.19, V:G.47
V08.13:	9 residues within 4Å: Chain Y: T.1, R.19, A.20, K.33, M.45, A.46, G.47, A.49, Y.170 8 PLIP interactions: 8 interactions with chain Y Hydrophobic interactions: Y:A.20, Y:A.49 Hydrogen bonds: Y:T.1, Y:R.19, Y:K.33, Y:G.47 Water bridges: Y:S.131, Y:S.131
V08.16:	5 residues within 4Å: Chain 1: T.1, T.20, R.45, S.46, G.47 4 PLIP interactions: 4 interactions with chain 1 Hydrophobic interactions: 1:T.20 Hydrogen bonds: 1:T.1, 1:G.47 Water bridges: 1:S.129

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shi, Y.M. et al., Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria. Nat.Chem. (2022)

Release Date

2022-04-13

Peptides

HLJ1_G0039880.mRNA.1.CDS.1: AO
BJ4_G0021480.mRNA.1.CDS.1: BP
HLJ1_G0048980.mRNA.1.CDS.1: CQ
20S proteasome: DR
BJ4_G0043800.mRNA.1.CDS.1: ES
Probable proteasome subunit alpha type-7: FT
BJ4_G0020160.mRNA.1.CDS.1: GU
Proteasome endopeptidase complex: HV
Proteasome endopeptidase complex: IW
Proteasome subunit beta: JX
Proteasome subunit beta type-5: KY
Proteasome endopeptidase complex: LZ
Proteasome subunit beta type-7: M0
Proteasome endopeptidase complex: 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

HLJ1_G0039880.mRNA.1.CDS.1

Toggle Identical (AO)

BJ4_G0021480.mRNA.1.CDS.1

Toggle Identical (BP)

HLJ1_G0048980.mRNA.1.CDS.1

Toggle Identical (CQ)

20S proteasome

Toggle Identical (DR)

BJ4_G0043800.mRNA.1.CDS.1

Toggle Identical (ES)

Probable proteasome subunit alpha type-7

Toggle Identical (FT)

BJ4_G0020160.mRNA.1.CDS.1

Toggle Identical (GU)

Proteasome endopeptidase complex

Toggle Identical (HV)

Proteasome endopeptidase complex

Toggle Identical (IW)

Proteasome subunit beta

Toggle Identical (JX)

Proteasome subunit beta type-5

Toggle Identical (KY)

Proteasome endopeptidase complex

Toggle Identical (LZ)

Proteasome subunit beta type-7

Toggle Identical (M0)

Proteasome endopeptidase complex

Toggle Identical (N1)

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Cartoon
Tube
Trace
Lines
Ball+Stick
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Spacefill
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Background

Transparent

Resolution

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