SMTL ID : 9aw7.1

Yeast 20S proteasome soaked with isolated TMC-95B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

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

Ligands

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

SO4.1: 4 residues within 4Å: Chain B: I.86, T.90, I.118, Y.122 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain B: G.121, Y.122, H.125, G.126, L.128 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain B: H.94, N.97, Y.98, T.101, Y.102, R.114 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain B: E.109, R.143, Y.144 Chain Q: R.70, E.71, D.72 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain C: Y.120, S.123 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain D: D.118 Chain E: R.82, V.83, N.86 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain D: R.166, Y.167, N.168 Chain E: L.56, S.57, S.58 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain E: F.99, R.107 Chain T: L.70, E.73, N.74 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain E: N.119, R.126, Y.128 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain F: A.121, H.122, Y.125 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain F: R.90, E.93, E.94, S.97 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain F: D.113 Chain G: L.95, K.98 Chain U: Q.69 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain G: Y.108, R.120 Chain O: Y.69 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain I: K.100 Chain W: M.66, Y.69, K.70 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain I: N.97, Y.98, T.101, R.114 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain J: S.123, V.126 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain K: R.166, N.168 Chain L: S.57, S.58 Ligand excluded by PLIP SO4.20: 6 residues within 4Å: Chain 0: L.70, E.73, N.74 Chain L: F.99, R.101, R.107 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain L: R.82, V.83, N.86 Ligand excluded by PLIP SO4.22: 7 residues within 4Å: Chain L: E.68, H.69, K.102, V.216, G.217, T.220, P.221 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain M: K.40, K.160, V.179, H.182, G.185, L.186 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain M: A.121 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain M: R.90, E.93, E.94, S.97 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain 1: Q.69 Chain M: D.113, Q.117 Chain N: F.73, L.95, K.98 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain N: Y.108 Chain V: Y.69 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain N: G.47, K.48, P.152, H.193 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain O: A.54, Q.57 Chain P: S.92, S.93, Y.96 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain O: Y.97 Ligands: SO4.34 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain O: T.1, A.46, G.47, G.128, S.129 Ligands: 01.30, SO4.33 Ligand excluded by PLIP SO4.35: 1 residues within 4Å: Ligands: 01.30 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain P: M.66, Y.69 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain C: V.91, S.95 Chain Q: A.62, N.63 Ligand excluded by PLIP SO4.39: 7 residues within 4Å: Chain P: V.36 Chain Q: Q.118, I.119, D.120, T.124, H.133 Ligands: SO4.41 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain Q: Q.99, N.101, Y.121 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain P: S.31 Chain Q: Q.118, H.133, G.134 Ligands: SO4.39 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain R: D.141 Chain X: Q.166, E.167, K.170 Ligand excluded by PLIP SO4.46: 1 residues within 4Å: Chain R: Y.90 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain R: Y.90 Chain S: Y.98, G.99, R.101 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain D: T.94, T.98, L.101 Chain R: Q.62 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain R: E.67, R.73 Ligand excluded by PLIP SO4.50: 1 residues within 4Å: Ligands: 01.42 Ligand excluded by PLIP SO4.51: 6 residues within 4Å: Chain R: T.1, A.46, G.47, G.130, S.131 Ligands: 01.42 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain S: G.56, Y.106 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain S: F.44, V.65, K.69 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain S: F.102, F.103 Chain T: M.107 Ligand excluded by PLIP SO4.56: 7 residues within 4Å: Chain R: S.28 Chain S: S.124, F.125, S.130, E.134, R.137 Ligands: 01.42 Ligand excluded by PLIP SO4.57: 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 SO4.58: 7 residues within 4Å: Chain T: N.26, G.38, V.39, E.40, S.196, K.210, N.211 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain E: Y.94 Chain T: Q.102 Ligand excluded by PLIP SO4.60: 1 residues within 4Å: Chain T: I.5 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain S: E.218 Chain T: R.161, E.162 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain T: S.54, W.111, N.112 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain T: T.7, S.29, G.31, R.190 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain T: D.47, N.48, D.201 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain O: F.88 Chain U: I.58, N.89 Ligand excluded by PLIP SO4.67: 2 residues within 4Å: Chain G: Y.106 Chain U: Y.61 Ligand excluded by PLIP SO4.68: 3 residues within 4Å: Chain U: Y.124, A.125, I.126 Ligand excluded by PLIP SO4.72: 6 residues within 4Å: Chain H: R.99 Chain V: A.54, Q.57 Chain W: S.92, S.93, Y.96 Ligand excluded by PLIP SO4.73: 2 residues within 4Å: Chain V: Y.97, G.128 Ligand excluded by PLIP SO4.74: 6 residues within 4Å: Chain V: S.112, I.113, H.114, D.120, L.127 Ligands: 01.102 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain J: S.95 Chain X: A.62, N.63 Ligand excluded by PLIP SO4.78: 6 residues within 4Å: Chain W: V.36 Chain X: Q.118, D.120, T.124, V.126, H.133 Ligand excluded by PLIP SO4.79: 4 residues within 4Å: Chain X: Q.99, V.100, N.101, Y.121 Ligand excluded by PLIP SO4.82: 3 residues within 4Å: Chain K: T.98 Chain Y: W.58, Q.62 Ligand excluded by PLIP SO4.83: 5 residues within 4Å: Chain Y: W.55, Y.90 Chain Z: Y.98, G.99, R.101 Ligand excluded by PLIP SO4.84: 2 residues within 4Å: Chain Y: Q.89, Y.90 Ligand excluded by PLIP SO4.85: 6 residues within 4Å: Chain Y: T.1, A.46, G.47, G.130, S.131 Ligands: 01.80 Ligand excluded by PLIP SO4.86: 1 residues within 4Å: Ligands: 01.80 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain Y: S.96, M.97, G.98 Ligand excluded by PLIP SO4.89: 1 residues within 4Å: Chain Z: Y.106 Ligand excluded by PLIP SO4.90: 4 residues within 4Å: Chain Z: N.3, Y.5, G.6, Y.106 Ligand excluded by PLIP SO4.91: 5 residues within 4Å: Chain Z: F.44, D.62, V.65, K.66, K.69 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain Z: E.215, F.216 Ligand excluded by PLIP SO4.93: 2 residues within 4Å: Chain 0: E.162 Chain Z: F.216 Ligand excluded by PLIP SO4.94: 9 residues within 4Å: Chain Z: H.108, S.124, F.125, D.126, S.130, E.132, E.134, R.137 Ligands: 01.80 Ligand excluded by PLIP SO4.95: 5 residues within 4Å: Chain 0: N.26, G.38, E.40, K.210, N.211 Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain 0: T.98, V.99, Q.102 Chain L: Y.94 Ligand excluded by PLIP SO4.97: 8 residues within 4Å: Chain 0: Y.30, L.33, R.35 Chain 1: A.127, G.128, S.131, T.132, Y.135 Ligand excluded by PLIP SO4.98: 2 residues within 4Å: Chain 0: P.4, I.5 Ligand excluded by PLIP SO4.99: 7 residues within 4Å: Chain 0: D.47, N.48, V.119, D.201, K.202, G.205 Ligands: SO4.101 Ligand excluded by PLIP SO4.100: 4 residues within 4Å: Chain 0: S.54, G.55, W.111, A.113 Ligand excluded by PLIP SO4.101: 6 residues within 4Å: Chain 0: D.47, N.48, D.82, A.83, A.86 Ligands: SO4.99 Ligand excluded by PLIP SO4.103: 3 residues within 4Å: Chain 1: I.58, N.89 Chain V: F.88 Ligand excluded by PLIP SO4.104: 6 residues within 4Å: Chain 1: T.1, S.46, G.47, G.128, S.129 Ligands: 01.102 Ligand excluded by PLIP SO4.105: 5 residues within 4Å: Chain 1: Y.137, N.141, D.153, F.154, H.157 Ligand excluded by PLIP

12 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain G: R.120, N.123 Chain O: Y.69 No protein-ligand interaction detected (PLIP) MG.13: 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.26: 3 residues within 4Å: Chain N: R.120, N.123 Chain V: Y.69 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:Y.69 MG.31: 5 residues within 4Å: Chain O: R.19, I.163, D.166, S.169 Chain Z: D.222 4 PLIP interactions: 3 interactions with chain O, 1 interactions with chain Z Metal complexes: O:I.163, O:D.166, O:S.169, Z:D.222 MG.36: 4 residues within 4Å: Chain P: A.175, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:A.175, P:D.178, P:S.181 MG.44: 6 residues within 4Å: Chain R: R.19, A.165, D.168, A.169, S.171 Chain W: D.205 4 PLIP interactions: 1 interactions with chain W, 3 interactions with chain R Metal complexes: W:D.205, R:A.165, R:D.168, R:S.171 MG.52: 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.71: 5 residues within 4Å: Chain S: D.222 Chain V: R.19, I.163, D.166, S.169 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain V Metal complexes: S:D.222, V:I.163, V:D.166, V:S.169 MG.75: 5 residues within 4Å: Chain W: A.175, D.178, A.179, S.181, D.205 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.178, W:S.181 MG.76: 6 residues within 4Å: Chain X: I.4, L.5, L.15, A.16, S.17, S.45 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:L.5, X:S.45 MG.81: 5 residues within 4Å: Chain P: D.205 Chain Y: 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.88: 7 residues within 4Å: Chain O: R.19 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:H.195, Z:V.198, Z:D.222

6 x 01: TMC-95B

01.30: 16 residues within 4Å: Chain O: T.1, S.20, T.21, Q.22, G.23, K.33, G.45, A.46, G.47, T.48, A.49 Chain P: D.125, L.126, I.127 Ligands: SO4.34, SO4.35 14 PLIP interactions: 10 interactions with chain O, 4 interactions with chain P Hydrophobic interactions: O:K.33, O:A.49, P:L.126, P:I.127 Hydrogen bonds: O:T.1, O:T.21, O:T.21, O:T.21, O:Q.22, O:G.23, O:G.47, O:A.49, P:D.125, P:D.125 01.42: 17 residues within 4Å: Chain R: T.1, A.20, T.21, A.22, K.33, M.45, G.47, G.48, A.49, S.96 Chain S: Y.106, D.126, P.127, V.128 Ligands: SO4.50, SO4.51, SO4.56 11 PLIP interactions: 7 interactions with chain R, 4 interactions with chain S Hydrophobic interactions: R:M.45, R:A.49, S:Y.106, S:P.127, S:V.128 Hydrogen bonds: R:T.1, R:T.21, R:T.21, R:G.47, R:A.49, S:D.126 01.65: 12 residues within 4Å: Chain O: H.114, H.116, S.118 Chain U: T.1, T.20, T.21, T.22, R.45, G.47, S.48, A.49, T.94 10 PLIP interactions: 7 interactions with chain U, 3 interactions with chain O Hydrophobic interactions: U:A.49, U:T.94, O:H.116 Hydrogen bonds: U:T.21, U:T.21, U:G.47, U:A.49, U:T.94, O:S.118 Water bridges: O:S.118 01.70: 15 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, G.23, A.27, K.33, G.45, A.46, G.47, T.48, A.49 Chain W: D.125, L.126, I.127 17 PLIP interactions: 13 interactions with chain V, 4 interactions with chain W Hydrophobic interactions: V:K.33, V:A.49, W:L.126, W:I.127 Hydrogen bonds: V:T.1, V:S.20, V:T.21, V:T.21, V:T.21, V:Q.22, V:G.23, V:G.47, V:A.49, W:D.125, W:D.125 Water bridges: V:T.1, V:T.1 01.80: 17 residues within 4Å: Chain Y: T.1, A.20, T.21, A.22, K.33, M.45, A.46, G.47, G.48, A.49, S.96 Chain Z: Y.106, D.126, V.128 Ligands: SO4.85, SO4.86, SO4.94 10 PLIP interactions: 6 interactions with chain Y, 4 interactions with chain Z Hydrophobic interactions: Y:M.45, Z:Y.106, Z:V.128 Hydrogen bonds: Y:T.1, Y:T.21, Y:T.21, Y:G.47, Y:A.49, Z:D.126 Water bridges: Z:S.130 01.102: 15 residues within 4Å: Chain 1: T.1, R.19, T.20, T.21, T.22, R.45, G.47, S.48, A.49, T.94 Chain V: H.114, H.116, S.118 Ligands: SO4.74, SO4.104 8 PLIP interactions: 7 interactions with chain 1, 1 interactions with chain V Hydrophobic interactions: 1:T.94 Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:G.47, 1:A.49, V:S.118 Water bridges: 1:A.50

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.43: 6 residues within 4Å: Chain R: S.96, G.98, Y.114, D.116, S.117, D.118 1 PLIP interactions: 1 interactions with chain R Hydrophobic interactions: R:D.116

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.69: 3 residues within 4Å: Chain S: Y.33 Chain T: H.149 Chain V: S.129 1 PLIP interactions: 1 interactions with chain T Salt bridges: T:H.149

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

PRE8 isoform 1: AH
PRE9 isoform 1: BI
PRE6 isoform 1: CJ
PUP2 isoform 1: DK
PRE5 isoform 1: EL
PRE10 isoform 1: FM
Proteasome subunit alpha type-1: GN
proteasome endopeptidase complex: OV
PUP3 isoform 1: PW
Proteasome subunit beta: QX
proteasome endopeptidase complex: RY
PRE7 isoform 1: SZ
Proteasome subunit beta: 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

PRE8 isoform 1

PRE9 isoform 1

PRE6 isoform 1

PUP2 isoform 1

PRE5 isoform 1

PRE10 isoform 1

Proteasome subunit alpha type-1

proteasome endopeptidase complex

PUP3 isoform 1

Proteasome subunit beta

proteasome endopeptidase complex

PRE7 isoform 1

Proteasome subunit beta

Proteasome subunit beta type-1

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