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

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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3oev.1 | 3okj.1 | 3sdi.1 | 3sdk.1 | 3shj.1 | 3tdd.1 | 3un4.1 | 3un8.1 | 3wxr.1 | 4cr2.1 | 4cr3.1 | 4cr4.1 | 4eu2.1 | 4fzc.1 | 4fzg.1 | 4g4s.1 | 4gk7.1 | 4hnp.1 | 4hrc.1 | 4hrd.1 | 4inr.1 | 4int.1 | 4inu.1 | 4j70.1 | 4jsq.1 | 4jsu.1 | 4jt0.1 | 4lqi.1 | 4ltc.1 | 4nnn.1 | 4nnw.1 | 4no1.1 | 4no6.1 | 4no8.1 | 4no9.1 | 4q1s.1 | 4qby.1 | 4qlq.1 | 4qls.1 | 4qlt.1 | 4qlu.1 | 4qlv.1 | 4qux.1 | 4quy.1 | 4qv0.1 | 4qv1.1 | 4qv3.1 | 4qv4.1 | 4qv5.1 | 4qv6.1 | 4qv7.1 | 4qv8.1 | 4qv9.1 | 4qvl.1 | 4qvm.1 | 4qvn.1 | 4qvp.1 | 4qvq.1 | 4qvv.1 | 4qvw.1 | 4qvy.1 | 4qw0.1 | 4qw1.1 | 4qw3.1 | 4qw4.1 | 4qw5.1 | 4qw6.1 | 4qw7.1 | 4qwf.1 | 4qwg.1 | 4qwi.1 | 4qwj.1 | 4qwk.1 | 4qwl.1 | 4qwr.1 | 4qws.1 | 4qwu.1 | 4qwx.1 | 4qxj.1 | 4qz0.1 | 4qz1.1 | 4qz2.1 | 4qz3.1 | 4qz4.1 | 4qz5.1 | 4qz6.1 | 4qz7.1 | 4qzw.1 | 4qzx.1 | 4qzz.1 | 4r00.1 | 4r02.1 | 4r17.1 | 4r18.1 | 4rur.1 | 4v7o.1 | 4v7o.2 | 4x6z.1 | 4y69.1 | 4y6a.1 | 4y6v.1 | 4y6z.1 | 4y70.1 | 4y74.1 | 4y75.1 | 4y77.1 | 4y78.1 | 4y7w.1 | 4y7x.1 | 4y7y.1 | 4y80.1 | 4y81.1 | 4y82.1 | 4y84.1 | 4y8g.1 | 4y8h.1 | 4y8i.1 | 4y8j.1 | 4y8k.1 | 4y8l.1 | 4y8m.1 | 4y8n.1 | 4y8o.1 | 4y8p.1 | 4y8q.1 | 4y8r.1 | 4y8s.1 | 4y8t.1 | 4y8u.1 | 4y9y.1 | 4y9z.1 | 4ya0.1 | 4ya1.1 | 4ya2.1 | 4ya3.1 | 4ya4.1 | 4ya5.1 | 4ya7.1 | 4ya9.1 | 4z1l.1 | 5a5b.1 | 5ahj.1 | 5bou.1 | 5bxl.1 | 5bxn.1 | 5cgf.1 | 5cgg.1 | 5cgh.1 | 5cgi.1 | 5cz4.1 | 5cz5.1 | 5cz6.1 | 5cz7.1 | 5cz8.1 | 5cz9.1 | 5cza.1 | 5d0s.1 | 5d0t.1 | 5d0v.1 | 5d0w.1 | 5d0x.1 | 5d0z.1 | 5dki.1 | 5dkj.1 | 5fg7.1 | 5fg9.1 | 5fga.1 | 5fgd.1 | 5fge.1 | 5fgf.1 | 5fgg.1 | 5fgh.1 | 5fgi.1 | 5fhs.1 | 5jhr.1 | 5jhs.1 | 5l52.1 | 5l54.1 | 5l55.1 | 5l5a.1 | 5l5b.1 | 5l5d.1 | 5l5e.1 | 5l5f.1 | 5l5h.1 | 5l5i.1 | 5l5j.1 | 5l5o.1 | 5l5p.1 | 5l5q.1 | 5l5r.1 | 5l5s.1 | 5l5t.1 | 5l5u.1 | 5l5v.1 | 5l5w.1 | 5l5x.1 | 5l5y.1 | 5l5z.1 | 5l60.1 | 5l61.1 | 5l62.1 | 5l63.1 | 5l64.1 | 5l65.1 | 5l66.1 | 5l67.1 | 5l68.1 | 5l69.1 | 5l6a.1 | 5l6b.1 | 5l6c.1 | 5lai.1 | 5laj.1 | 5ltt.1 | 5m2b.1 | 5mp9.1 | 5mpa.1 | 5mpb.1 | 5mpc.1 | 5nif.1 | 5wvi.1 | 5wvk.1 | 6ef0.1 | 6ef1.1 | 6ef3.1 | 6fvt.1 | 6fvu.1 | 6fvv.1 | 6fvw.1 | 6fvx.1 | 6fvy.1 | 6g7f.1 | 6g8m.1 | 6g8n.1 | 6gop.1 | 6h39.1 | 6htb.1 | 6htc.1 | 6htd.1 | 6htp.1 | 6htr.1 | 6hub.1 | 6huc.1 | 6huq.1 | 6huu.1 | 6huv.1 | 6hv3.1 | 6hv4.1 | 6hv5.1 | 6hv7.1 | 6hva.1 | 6hvr.1 | 6hvs.1 | 6hvt.1 | 6hvu.1 | 6hvv.1 | 6hvw.1 | 6hvx.1 | 6hvy.1 | 6hw0.1 | 6hw3.1 | 6hw4.1 | 6hw5.1 | 6hw6.1 | 6hw7.1 | 6hw8.1 | 6hw9.1 | 6hwa.1 | 6hwb.1 | 6hwc.1 | 6hwd.1 | 6hwe.1 | 6hwf.1 | 6j2c.1 | 6j2n.1 | 6j2q.1 | 6j2x.1 | 6j30.1 | 6zou.1 | 6zp6.1 | 6zp8.1 | 7ls5.1 | 7ls6.1 | 7lsx.1 | 7qo3.1 | 7qo5.1 | 7qo6.1 | 7tej.1 | 7teo.1 | 8bw1.1 | 8ohz.1 | 8oi1.1 | 8olr.1 | 8t08.1 | 8t0m.1 | 8u6y.1 | 8u7u.1

Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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Extreme

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