SMTL ID : 9aw5.1

Yeast 20S proteasome soaked with MA9 fraction E/F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.44 Å

Oligo State

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

Ligands

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

SO4.1: 3 residues within 4Å: Chain B: E.109, Y.144 Chain Q: R.70 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain C: S.123, V.126 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain D: R.166, Y.167, N.168 Chain E: L.56, S.57, S.58 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain E: R.82, V.83, N.86 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain E: D.80, N.119, R.126, Y.128 Ligand excluded by PLIP SO4.6: 8 residues within 4Å: Chain F: D.113, Q.117 Chain G: F.73, R.91, A.94, L.95, K.98 Chain U: Q.69 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain F: A.121, H.122, Y.125 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain F: R.90, E.93, E.94, S.97 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain G: F.104, Y.108 Chain O: Y.69 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain I: E.109 Chain X: R.70, E.71 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain J: Y.120, S.123, V.126 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain L: R.82, V.83, N.86 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain L: H.69, K.102, G.217, D.219, T.220, P.221 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain M: D.113 Chain N: F.73, R.91, L.95, K.98 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain M: K.40, K.160, V.179, H.182, G.185, L.186 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain M: A.121, Y.125 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain M: R.90, E.93, E.94, S.97 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain N: K.107, Y.108 Chain V: Y.69 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain O: A.54, Q.57 Chain P: S.92, S.93, Y.96 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain O: F.88 Chain U: I.58, N.89 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain O: Y.97, G.128 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain P: M.66, Y.69, K.70 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain O: T.21, Q.22 Chain P: D.125, C.129 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: Q.94 Chain Q: A.62, N.63, L.66 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain Q: L.163, Q.166, E.167 Chain Y: D.141, S.142 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain R: S.96, M.97, G.98, Y.114, D.116 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain R: Q.89, Y.90 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain R: W.55, Y.90 Chain S: Y.98, G.99 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: T.94, T.98 Chain R: Q.62 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain S: Y.106 Ligands: 01.28 Ligand excluded by PLIP SO4.36: 9 residues within 4Å: Chain R: S.28 Chain S: H.108, S.124, F.125, D.126, S.130, E.134, R.137 Ligands: 01.28 Ligand excluded by PLIP SO4.37: 7 residues within 4Å: Chain T: N.26, G.38, V.39, E.40, S.196, K.210, N.211 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain E: R.101, R.107 Chain T: L.70, E.73, N.74 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain E: Y.94, V.98 Chain T: Y.95, T.98, Q.102 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain T: I.5, Y.30 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain T: R.161, E.162 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain T: N.112, A.113 Ligand excluded by PLIP SO4.43: 7 residues within 4Å: Chain T: Y.30, R.35 Chain U: A.127, G.128, S.131, T.132, Y.135 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain T: Y.30 Chain U: S.46, L.115, G.128 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain V: A.54, Q.57 Chain W: S.92, S.93, Y.96 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain V: Y.97, G.128, S.129 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain W: M.66, Y.69 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain W: R.99, L.126, I.127 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain J: S.95 Chain X: A.62, N.63 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain Y: M.97, G.98, D.116 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain K: T.98 Chain Y: W.58, Q.62 Ligand excluded by PLIP SO4.56: 4 residues within 4Å: Chain Y: Y.90 Chain Z: Y.98, G.99, R.101 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain Y: Q.89, Y.90 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain Z: Y.106, V.107 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain Z: N.3, Y.5, Y.106 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain 0: E.162 Chain Z: Y.39, F.216 Ligand excluded by PLIP SO4.62: 8 residues within 4Å: Chain Y: S.28 Chain Z: S.124, F.125, D.126, S.130, E.134, R.137 Ligands: 01.52 Ligand excluded by PLIP SO4.63: 5 residues within 4Å: Chain 0: N.26, G.38, E.40, K.210, N.211 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain 0: V.99, Q.102 Chain L: Y.94, V.98 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain 0: L.70, E.73 Chain L: R.107 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain 0: Q.3, P.4, I.5 Ligand excluded by PLIP SO4.67: 6 residues within 4Å: Chain 0: D.47, N.48, V.119, D.201, K.202, G.205 Ligand excluded by PLIP SO4.68: 1 residues within 4Å: Chain 0: W.111 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain 1: I.58, N.89 Chain V: F.88 Ligand excluded by PLIP SO4.70: 3 residues within 4Å: Chain 1: S.46, L.115 Ligands: SO4.71 Ligand excluded by PLIP SO4.71: 9 residues within 4Å: Chain 0: Y.30, R.35 Chain 1: I.126, A.127, G.128, S.131, T.132, Y.135 Ligands: SO4.70 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 7 residues within 4Å: Chain O: G.162, I.163, W.164, D.166, L.167, S.169 Chain Z: D.222 3 PLIP interactions: 1 interactions with chain Z, 2 interactions with chain O Metal complexes: Z:D.222, O:I.163, O:D.166 MG.23: 5 residues within 4Å: Chain P: A.175, D.178, A.179, S.181, D.205 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.178, P:S.181 MG.29: 6 residues within 4Å: Chain R: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 4 PLIP interactions: 3 interactions with chain R, 1 interactions with chain W Metal complexes: R:A.165, R:H.166, R:D.168, W:D.205 MG.34: 6 residues within 4Å: Chain S: R.28, T.192, H.195, I.196, V.198, D.222 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:T.192, S:H.195, S:V.198 MG.45: 5 residues within 4Å: Chain S: D.222 Chain V: I.163, W.164, D.166, S.169 3 PLIP interactions: 1 interactions with chain S, 2 interactions with chain V Metal complexes: S:D.222, V:I.163, V:D.166 MG.48: 4 residues within 4Å: Chain W: A.175, 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.53: 6 residues within 4Å: Chain P: D.205 Chain Y: R.19, A.165, D.168, A.169, S.171 4 PLIP interactions: 1 interactions with chain P, 3 interactions with chain Y Metal complexes: P:D.205, Y:A.165, Y:D.168, Y:S.171 MG.58: 6 residues within 4Å: Chain O: R.19 Chain Z: R.28, T.192, H.195, V.198, D.222 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198

2 x 01: (10S,11R,12S,15S,18S)-15-(2-amino-2-oxoethyl)-10,11,23-trihydroxy-18-{[(3R)-3-methyl-2-oxopentanoyl]amino}-9,14,17-trioxo-N-[(1Z)-prop-1-en-1-yl]-8,13,16-triazatetracyclo[18.3.1.0(2,7).0(6,10)]tetracosa-1(24),2,4,6,20,22-hexaene-12-carboxamide

01.28: 15 residues within 4Å: Chain R: T.1, A.20, T.21, A.22, A.27, K.33, G.47, G.48, A.49, S.96 Chain S: D.126, P.127, V.128 Ligands: SO4.35, SO4.36 6 PLIP interactions: 5 interactions with chain R, 1 interactions with chain S Hydrophobic interactions: R:A.20, R:A.49, S:V.128 Hydrogen bonds: R:T.1, R:T.21, R:G.47 01.52: 15 residues within 4Å: Chain Y: T.1, A.20, T.21, A.22, A.27, K.33, G.47, G.48, A.49, S.96 Chain Z: Y.106, D.126, P.127, V.128 Ligands: SO4.62 11 PLIP interactions: 4 interactions with chain Z, 7 interactions with chain Y Hydrophobic interactions: Z:Y.106, Z:Y.106, Z:V.128, Y:A.20, Y:A.49 Hydrogen bonds: Z:D.126, Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:A.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meneghello, R. et al., High-throughput protein crystallography to empower natural product-based drug discovery. To be published

Release Date

2025-03-19

Peptides

Proteasome subunit alpha type-2: AH
Proteasome subunit alpha type-3: BI
Proteasome subunit alpha type-4: CJ
Proteasome subunit alpha type-5: DK
Proteasome subunit alpha type-6: EL
Probable proteasome subunit alpha type-7: FM
Proteasome subunit alpha type-1: GN
Proteasome subunit beta type-2: OV
Proteasome subunit beta type-3: PW
Proteasome subunit beta type-4: QX
Proteasome subunit beta type-5: RY
Proteasome subunit beta type-6: SZ
Proteasome subunit beta type-7: T0
Proteasome subunit beta type-1: U1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
O

B
B

I
P

C
C

J
Q

D
D

K
R

E
E

L
S

F
F

M
T

G
G

N
U

O
H

V
V

P
I

W
W

Q
J

X
X

R
K

Y
Y

S
L

Z
Z

T
M

0
a

U
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

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