SMTL ID : 9j99.1

Substrate-engaged TOM complex from yeast

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

26 x UND: UNDECANE(Non-functional Binders)(Non-covalent)

UND.1: 1 residues within 4Å: Ligands: UND.6 Ligand excluded by PLIP UND.6: 7 residues within 4Å: Chain A: S.151, L.167, Q.169, V.180, T.182 Ligands: UND.1, UND.10 Ligand excluded by PLIP UND.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UND.8: 1 residues within 4Å: Chain A: A.197 Ligand excluded by PLIP UND.10: 1 residues within 4Å: Ligands: UND.6 Ligand excluded by PLIP UND.13: 1 residues within 4Å: Chain B: R.89 Ligand excluded by PLIP UND.16: 2 residues within 4Å: Chain A: L.209 Chain C: W.42 Ligand excluded by PLIP UND.17: 1 residues within 4Å: Ligands: PC1.5 Ligand excluded by PLIP UND.18: 1 residues within 4Å: Chain D: L.53 Ligand excluded by PLIP UND.22: 1 residues within 4Å: Chain D: V.43 Ligand excluded by PLIP UND.23: 3 residues within 4Å: Chain D: V.46, A.47 Ligands: PC1.21 Ligand excluded by PLIP UND.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UND.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UND.27: 3 residues within 4Å: Chain E: A.42, H.43 Ligands: PC1.2 Ligand excluded by PLIP UND.31: 1 residues within 4Å: Ligands: PC1.28 Ligand excluded by PLIP UND.34: 6 residues within 4Å: Chain F: V.137, G.139, L.155, I.157 Chain J: H.29, W.32 Ligand excluded by PLIP UND.38: 2 residues within 4Å: Chain F: T.182 Ligands: PC1.28 Ligand excluded by PLIP UND.39: 2 residues within 4Å: Chain F: A.197 Ligands: PC1.29 Ligand excluded by PLIP UND.40: 4 residues within 4Å: Chain F: L.141, Y.143, S.151, V.153 Ligand excluded by PLIP UND.44: 1 residues within 4Å: Chain I: S.51 Ligand excluded by PLIP UND.45: 3 residues within 4Å: Chain I: V.46, Q.50 Ligands: PC1.35 Ligand excluded by PLIP UND.46: 2 residues within 4Å: Chain F: F.347 Ligands: PC1.37 Ligand excluded by PLIP UND.47: 2 residues within 4Å: Chain J: P.58 Ligands: PC1.48 Ligand excluded by PLIP UND.49: 1 residues within 4Å: Chain J: A.42 Ligand excluded by PLIP UND.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UND.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

25 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

PC1.2: 3 residues within 4Å: Chain A: L.125, Y.143 Ligands: UND.27 Ligand excluded by PLIP PC1.3: 5 residues within 4Å: Chain A: V.137, G.139, L.155, P.185 Ligands: PC1.12 Ligand excluded by PLIP PC1.4: 10 residues within 4Å: Chain A: L.211, Y.232, L.233, T.234, G.247, Q.248, L.249 Chain C: Q.27, F.34, L.35 Ligand excluded by PLIP PC1.5: 9 residues within 4Å: Chain A: K.148, Y.171, A.173, S.174, F.176, A.199, L.213, T.215 Ligands: UND.17 Ligand excluded by PLIP PC1.9: 6 residues within 4Å: Chain A: T.301, I.303, D.319, S.320, G.322 Ligands: PC1.19 Ligand excluded by PLIP PC1.11: 13 residues within 4Å: Chain A: H.102, F.104, K.113, Y.114, D.132, N.133 Chain E: L.51, L.54, S.55 Chain G: T.93, G.96, W.100 Ligands: PC1.42 Ligand excluded by PLIP PC1.12: 9 residues within 4Å: Chain A: I.157, S.158, Q.161, P.162, T.163, N.184, S.186 Chain E: H.25 Ligands: PC1.3 Ligand excluded by PLIP PC1.14: 8 residues within 4Å: Chain B: A.106, L.107, G.110, Q.121 Chain D: L.61 Ligands: PC1.15, PC1.20, PC1.48 Ligand excluded by PLIP PC1.15: 8 residues within 4Å: Chain B: S.114, L.118, Q.121 Chain F: F.359 Chain J: L.57 Ligands: PC1.14, PC1.33, PC1.48 Ligand excluded by PLIP PC1.19: 3 residues within 4Å: Chain A: F.347 Chain D: F.41 Ligands: PC1.9 Ligand excluded by PLIP PC1.20: 14 residues within 4Å: Chain A: A.269, I.303, G.304, Y.314, G.316, L.318 Chain B: L.109, L.113 Chain D: F.48, M.54, M.56, L.57, P.59 Ligands: PC1.14 Ligand excluded by PLIP PC1.21: 11 residues within 4Å: Chain A: T.234, Y.236, K.239, W.243, F.245, R.261 Chain D: Q.50, S.51, P.52, D.55 Ligands: UND.23 Ligand excluded by PLIP PC1.26: 4 residues within 4Å: Chain A: L.135 Chain E: V.27, Y.30 Ligands: PC1.42 Ligand excluded by PLIP PC1.28: 7 residues within 4Å: Chain F: N.149, S.151, Q.169, V.180, T.182 Ligands: UND.31, UND.38 Ligand excluded by PLIP PC1.29: 5 residues within 4Å: Chain F: V.178, T.215 Chain H: A.32, W.36 Ligands: UND.39 Ligand excluded by PLIP PC1.30: 24 residues within 4Å: Chain A: L.84, R.85, F.104, S.105, I.106, L.328, R.330, V.338, G.356, L.357 Chain B: T.104, A.119, Q.122 Chain F: R.85, A.86, I.106, R.330, V.332, V.338, F.340, L.357 Chain G: W.100, T.104, L.107 Ligand excluded by PLIP PC1.32: 8 residues within 4Å: Chain F: I.157, S.158, Q.161, P.162, T.163, N.184 Chain J: H.25, N.26 Ligand excluded by PLIP PC1.33: 13 residues within 4Å: Chain B: G.96, N.97, W.100, T.103 Chain F: K.113, Y.114, N.133, D.134, L.135 Chain J: L.54, S.55, P.56 Ligands: PC1.15 Ligand excluded by PLIP PC1.35: 13 residues within 4Å: Chain F: Y.236, K.239, D.242, W.243, F.245, L.255, R.261, T.273, L.275 Chain I: F.42, Q.50 Ligands: PC1.36, UND.45 Ligand excluded by PLIP PC1.36: 10 residues within 4Å: Chain F: L.211, G.212, Y.232, L.233, T.234, G.247, I.256 Chain H: Q.27, L.35 Ligands: PC1.35 Ligand excluded by PLIP PC1.37: 9 residues within 4Å: Chain F: T.301, I.303, D.319, S.320, H.346, F.347, N.349 Chain G: L.98 Ligands: UND.46 Ligand excluded by PLIP PC1.41: 3 residues within 4Å: Chain G: A.106, S.114, Q.121 Ligand excluded by PLIP PC1.42: 6 residues within 4Å: Chain A: L.135 Chain G: R.89, F.92, T.93 Ligands: PC1.11, PC1.26 Ligand excluded by PLIP PC1.43: 8 residues within 4Å: Chain F: I.303, G.304, Y.307, Y.314, G.316 Chain I: M.56, L.57, P.59 Ligand excluded by PLIP PC1.48: 3 residues within 4Å: Ligands: PC1.14, PC1.15, UND.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y.Q. et al., Substrate-engaged TOM complex from yeast. To Be Published

Release Date

2025-09-10

Peptides

Mitochondrial import receptor subunit TOM40: AF
Mitochondrial import receptor subunit TOM22: BG
Mitochondrial import receptor subunit TOM5: CH
Mitochondrial import receptor subunit TOM6: DI
Mitochondrial import receptor subunit TOM7: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
I

B
B

G
J

C
C

H
K

D
D

I
L

E
E

J
M

Membrane

We predict this structure to be a membrane protein.
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Mitochondrial import receptor subunit TOM40

Mitochondrial import receptor subunit TOM22

Mitochondrial import receptor subunit TOM5

Mitochondrial import receptor subunit TOM6

Mitochondrial import receptor subunit TOM7

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