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SMTL ID : 9qd2.1

Yeast 20S proteasome mutant: beta1_G128V (b1-propeptide deleted) in complex with MG132

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x P6S- LEU- LEU- 01: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE(Non-covalent)

P6S-LEU-LEU-01.1:	22 residues within 4Å: Chain H: T.1, I.2, D.16, S.19, T.20, Q.21, 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, L.126, I.127 19 PLIP interactions: 4 interactions with chain I, 15 interactions with chain H Hydrophobic interactions: I:L.126, I:I.127, H:I.2, H:Q.21, H:A.45, H:A.48 Hydrogen bonds: I:D.125, I:D.125, H:T.20, H:T.20, H:Q.21, H:G.46, H:G.46, H:A.48, H:S.128, H:G.129, H:S.168, H:S.168 Salt bridges: H:K.32
P6S-LEU-LEU-01.2:	19 residues within 4Å: Chain K: T.1, D.16, A.19, T.20, A.26, K.32, M.44, A.45, G.46, G.47, A.48, G.129, S.130, G.131, Y.169, S.170 Chain L: Y.106, D.126, S.130 17 PLIP interactions: 3 interactions with chain L, 14 interactions with chain K Hydrophobic interactions: L:Y.106, L:D.126, K:A.19, K:A.26, K:M.44, K:A.45, K:A.48 Hydrogen bonds: L:D.126, K:T.20, K:T.20, K:G.46, K:G.46, K:G.46, K:A.48, K:G.131, K:S.170 Salt bridges: K:K.32
P6S-LEU-LEU-01.3:	21 residues within 4Å: Chain H: H.113, S.117 Chain N: S.1, I.2, D.16, T.19, T.20, T.21, K.32, R.44, S.45, G.46, S.47, A.48, T.51, A.126, V.127, S.128, D.165, S.167, S.168 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:I.2, N:T.19, N:A.48 Hydrogen bonds: N:T.20, N:T.20, N:G.46, N:G.46, N:A.48, N:S.168 Salt bridges: N:K.32
P6S-LEU-LEU-01.4:	22 residues within 4Å: Chain V: T.1, I.2, D.16, S.19, T.20, Q.21, 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 W: D.125, L.126, I.127 17 PLIP interactions: 14 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:I.2, V:Q.21, V:A.45, V:A.48, W:I.127 Hydrogen bonds: V:T.20, V:T.20, V:Q.21, V:G.46, V:G.46, V:A.48, V:S.128, V:G.129, V:S.168, W:D.125, W:D.125 Salt bridges: V:K.32
P6S-LEU-LEU-01.5:	20 residues within 4Å: Chain Y: T.1, D.16, A.19, T.20, A.26, K.32, M.44, A.45, G.46, G.47, A.48, G.129, S.130, G.131, Y.169, S.170 Chain Z: Y.106, D.126, P.127, S.130 19 PLIP interactions: 15 interactions with chain Y, 4 interactions with chain Z Hydrophobic interactions: Y:A.19, Y:A.26, Y:M.44, Y:A.45, Y:A.48, Z:Y.106, Z:D.126, Z:P.127 Hydrogen bonds: Y:T.20, Y:T.20, Y:G.46, Y:G.46, Y:G.46, Y:A.48, Y:S.130, Y:G.131, Y:S.170, Z:D.126 Salt bridges: Y:K.32
P6S-LEU-LEU-01.6:	22 residues within 4Å: Chain 1: S.1, I.2, D.16, T.19, T.20, T.21, K.32, R.44, S.45, G.46, S.47, A.48, T.51, A.126, V.127, S.128, S.167, S.168 Chain V: H.113, H.115, S.117 Ligands: CL.16 11 PLIP interactions: 11 interactions with chain 1 Hydrophobic interactions: 1:I.2, 1:T.19, 1:A.48 Hydrogen bonds: 1:T.20, 1:T.20, 1:G.46, 1:G.46, 1:A.48, 1:S.128, 1:D.165 Salt bridges: 1:K.32

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7:	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.10:	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.11:	3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP)
MG.14:	6 residues within 4Å: Chain H: R.18 Chain Z: R.28, T.192, H.195, V.198, D.222 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.192, Z:V.198

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.8:	3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.68 Ligand excluded by PLIP
CL.9:	3 residues within 4Å: Chain G: F.73, C.74, K.98 Ligand excluded by PLIP
CL.12:	3 residues within 4Å: Chain N: T.30, R.44, Q.52 Ligand excluded by PLIP
CL.13:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.68 Ligand excluded by PLIP
CL.16:	4 residues within 4Å: Chain 1: T.30, R.44, Q.52 Ligands: P6S-LEU-LEU-01.6 Ligand excluded by PLIP

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

MES.15:

3 residues within 4Å:

Chain 0: R.174, E.175
Chain Z: Y.39

2 PLIP interactions:

1 interactions with chain Z, 1 interactions with chain 0

pi-Cation interactions: Z:F.216
Hydrogen bonds: 0:E.175

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Huber, E.M. et al., Proteasome-associated autoinflammatory syndromes: The impact of mutations in proteasome subunits on particle assembly, structure, and activity. Structure (2025)

Release Date

2025-10-08

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-2: 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-2

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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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 | 7o2l.1 | 7qo3.1 | 7qo5.1 | 7qo6.1 | 7tej.1 | 7teo.1 | 8bw1.1 | 8ohz.1 | 8oi1.1 | 8olr.1 | 8rhj.1 | 8rhk.1 | 8rhl.1 | 8rvl.1 | 8rvo.1 | 8rvp.1 | 8rvq.1 | 8t08.1 | 8t0m.1 | 8u6y.1 | 8u7u.1 | 9aw3.1 | 9aw5.1 | 9aw6.1 | 9aw7.1 | 9c97.1 | 9c98.1 | 9cgc.1 | 9d0t.1 | 9d35.1 | 9d3i.1 | 9d4c.1 | 9d4u.1 | 9ey9.1 | 9frw.1 | 9fst.1 | 9fsu.1 | 9fsv.1 | 9ft0.1 | 9ft1.1 | 9gbk.1 | 9qaf.1 | 9qai.1 | 9qb1.1 | 9qb4.1 | 9qbe.1 | 9qbi.1 | 9qbo.1 | 9qbw.1 | 9qby.1 | 9qc9.1 | 9qcf.1 | 9qck.1 | 9qdf.1 | 9qds.1

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

Background

Transparent

Resolution

Low
Medium
High
Extreme

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