SMTL ID : 8oi1.1

Yeast 20S proteasome in complex with a photoswitchable cepafungin derivative (transCep4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

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

Ligands

11 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.17, G:A.132, G:M.134 MG.3: 4 residues within 4Å: Chain I: A.175, D.178, S.181, D.205 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.178, I:S.181 MG.4: 5 residues within 4Å: Chain I: R.28, A.179, D.205 Chain Y: A.169 Ligands: MG.16 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP) MG.7: 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: 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.8: 3 residues within 4Å: Chain K: I.82, N.85, L.86 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain 0: L.47 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 MG.10: 3 residues within 4Å: Chain H: Q.91 Chain N: D.51, N.92 No protein-ligand interaction detected (PLIP) MG.14: 8 residues within 4Å: Chain L: D.222 Chain V: R.19, G.162, I.163, W.164, D.166, L.167, S.169 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, V:S.169, L:D.222 MG.16: 8 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, D.168, A.169, S.171 Ligands: MG.4 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:D.168, Y:S.171, I:D.205 MG.17: 6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198

4 x VOX: ~{N}-[(2~{S},3~{R})-1-[[(5~{S},8~{S},10~{S})-5-methyl-10-oxidanyl-2,7-bis(oxidanylidene)-1,6-diazacyclododec-8-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-7-[4-[2-(4-methylphenyl)hydrazinyl]phenyl]heptanamide(Covalent)

VOX.2: 12 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, K.33, G.47, T.48, A.49 Chain I: R.99, F.104, D.125, L.126 14 PLIP interactions: 8 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:T.1, H:A.49, I:L.126, I:L.126 Hydrogen bonds: H:T.21, H:T.21, H:Q.22, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125, I:D.125 pi-Stacking: I:F.104 VOX.6: 14 residues within 4Å: Chain K: T.1, A.20, T.21, K.33, G.47, G.48, A.49 Chain L: Y.5, F.102, F.103, P.104, Y.106, D.126, P.127 16 PLIP interactions: 8 interactions with chain L, 8 interactions with chain K Hydrophobic interactions: L:F.103, L:F.103, L:P.104, L:Y.106, L:P.127, K:T.1, K:A.20, K:A.49 Hydrogen bonds: L:Y.5, L:D.126, L:D.126, K:T.21, K:T.21, K:G.47, K:G.47, K:A.49 VOX.13: 12 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, K.33, G.47, T.48, A.49 Chain W: R.99, P.102, F.104, D.125 14 PLIP interactions: 9 interactions with chain V, 5 interactions with chain W Hydrophobic interactions: V:T.1, V:T.48, W:P.102 Hydrogen bonds: V:T.21, V:T.21, V:Q.22, V:G.47, V:G.47, V:A.49, V:S.129, W:D.125, W:D.125, W:D.125 pi-Stacking: W:F.104 VOX.15: 13 residues within 4Å: Chain Y: T.1, A.20, T.21, K.33, G.47, G.48, A.49 Chain Z: Y.5, F.102, F.103, P.104, Y.106, D.126 15 PLIP interactions: 8 interactions with chain Y, 7 interactions with chain Z Hydrophobic interactions: Y:T.1, Y:A.20, Y:A.49, Z:Y.5, Z:F.103, Z:P.104, Z:Y.106 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49, Z:Y.5, Z:D.126, Z:D.126

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

CL.11: 3 residues within 4Å: Chain N: T.31, R.45, Q.53 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain 1: T.31, R.45, A.49, Q.53 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 5 residues within 4Å: Chain N: T.1, S.46, G.47, G.128, S.129 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:T.1, N:T.1, N:G.47, N:G.47, N:S.129, N:S.129 SO4.19: 5 residues within 4Å: Chain 1: T.1, S.46, G.47, G.128, S.129 4 PLIP interactions: 4 interactions with chain 1 Hydrogen bonds: 1:T.1, 1:T.1, 1:G.47, 1:S.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morstein, J. et al., Optical Control of Proteasomal Protein Degradation with a Photoswitchable Lipopeptide. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2023-12-27

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

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit alpha type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-1

Related Entries With Identical Sequence