SMTL ID : 7vby.1

Tom core complex with Tom20 and Tom22 subunits.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

PC1.1: 23 residues within 4Å: Chain A: L.229, L.231, L.250, A.251, G.252, K.253, Y.254, L.256, N.257, W.259, A.261, T.262, V.263, L.265, M.270, A.272, T.273, Y.274 Chain D: F.52, V.56, R.60 Chain F: Y.34 Ligands: UND.9 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.250, A:Y.254, A:Y.254, A:W.259, A:V.263, A:V.263, A:V.263, A:Y.274, A:Y.274, D:F.52, D:F.52 Hydrogen bonds: A:Y.254 Salt bridges: D:R.60, D:R.60 PC1.2: 19 residues within 4Å: Chain A: T.297, V.318, D.319, S.320, N.321, W.322, V.324, H.347, R.348 Chain D: R.38, R.43, N.44, L.47, N.48, L.51, W.57 Chain I: I.87, S.91, L.95 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.322, A:W.322 Salt bridges: A:R.348, D:R.38, D:R.43 PC1.3: 16 residues within 4Å: Chain A: H.117, Y.129, F.131, M.154, D.155, N.156, S.157, G.158 Chain H: Y.78, R.79, R.82 Chain J: W.25, L.52, L.53 Ligands: PC1.18, UND.23 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain J, 1 interactions with chain A Salt bridges: H:R.82, H:R.82 Hydrophobic interactions: J:W.25, J:L.53, A:F.131 PC1.6: 20 residues within 4Å: Chain B: R.38, R.43, N.44, L.47, N.48, L.51, A.54, G.55, W.57, L.58 Chain G: T.297, V.299, S.300, F.301, V.318, D.319, S.320, N.321, W.322, R.348 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:A.54, G:V.299, G:F.301 Salt bridges: B:R.38, B:R.43, G:R.348 PC1.8: 8 residues within 4Å: Chain C: L.37, T.41, L.45 Chain G: I.225, L.229, L.231, Y.254 Ligands: PC1.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.41 PC1.12: 41 residues within 4Å: Chain A: V.101, F.314, A.326, T.327, L.328, K.330, L.332, L.339, L.341, G.342, A.343, F.356, L.358 Chain G: V.101, L.103, F.314, A.326, T.327, L.328, K.330, L.332, L.339, L.341, G.342, A.343, F.356, L.358 Chain H: M.93, I.94, L.97, P.98, F.101, E.102, K.105 Chain I: M.93, I.94, L.97, P.98, F.101, E.102, K.105 21 PLIP interactions: 3 interactions with chain I, 7 interactions with chain G, 7 interactions with chain A, 4 interactions with chain H Hydrophobic interactions: I:L.97, I:P.98, G:V.101, G:F.314, G:A.326, G:L.328, G:A.343, G:F.356, A:V.101, A:L.339, A:A.343, A:L.358, A:L.358, H:L.97, H:P.98, H:P.98 Salt bridges: I:K.105, G:K.330, A:K.330, A:K.330, H:K.105 PC1.13: 24 residues within 4Å: Chain B: L.49, F.52, V.56, R.60 Chain G: L.229, L.231, L.250, A.251, G.252, K.253, Y.254, L.256, N.257, W.259, A.261, T.262, V.263, L.265, M.270, A.272, T.273, Y.274 Ligands: UND.7, PC1.8 17 PLIP interactions: 12 interactions with chain G, 5 interactions with chain B Hydrophobic interactions: G:L.229, G:L.231, G:L.250, G:Y.254, G:Y.254, G:W.259, G:A.261, G:V.263, G:V.263, G:Y.274, B:L.49, B:L.49, B:V.56 Hydrogen bonds: G:Y.254, G:N.257 Salt bridges: B:R.60, B:R.60 PC1.14: 13 residues within 4Å: Chain E: Q.13, L.15, F.16, K.17, S.19, Q.20, I.23 Chain G: K.184, F.185, W.188, P.208, D.209, V.210 8 PLIP interactions: 3 interactions with chain G, 5 interactions with chain E Hydrophobic interactions: G:W.188, G:P.208, E:L.15, E:F.16 Hydrogen bonds: G:V.210, E:Q.13, E:Q.20 Salt bridges: E:K.17 PC1.18: 19 residues within 4Å: Chain A: V.105, K.107, H.117, E.126, S.127, Y.129, N.156, I.360 Chain G: N.350 Chain H: A.74, M.77, Y.78, S.81, R.82, L.85, W.86, T.89 Chain J: L.53 Ligands: PC1.3 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain H Hydrophobic interactions: A:Y.129, H:R.82, H:L.85 Hydrogen bonds: A:N.156 Salt bridges: H:R.82, H:R.82 pi-Cation interactions: H:W.86 PC1.20: 16 residues within 4Å: Chain E: W.25, V.49, L.52, L.53 Chain G: Y.129, F.131, M.154, D.155, N.156, S.157, G.158 Chain I: Y.78, R.79, R.82 Ligands: UND.10, PC1.21 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:R.79 Salt bridges: I:R.82, I:R.82 Hydrophobic interactions: E:W.25, E:L.53 PC1.21: 20 residues within 4Å: Chain A: N.350 Chain E: L.53, W.54 Chain G: V.105, H.117, E.126, S.127, Y.129, N.156, I.360 Chain I: Y.78, S.81, R.82, L.85, W.86, T.89, V.100, F.101 Ligands: PC1.20, UND.22 9 PLIP interactions: 7 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: I:Y.78, I:R.82, I:T.89, G:Y.129 Salt bridges: I:R.82, I:R.82 pi-Cation interactions: I:W.86, I:W.86 Hydrogen bonds: G:N.156

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

UND.4: 4 residues within 4Å: Chain A: Y.303, L.305 Chain D: D.66 Chain I: V.99 No protein-ligand interaction detected (PLIP) UND.5: 6 residues within 4Å: Chain A: A.201, A.219, Y.221 Chain F: F.31, V.35, R.39 No protein-ligand interaction detected (PLIP) UND.7: 6 residues within 4Å: Chain B: F.52, A.53, V.56, W.57, R.60 Ligands: PC1.13 No protein-ligand interaction detected (PLIP) UND.9: 6 residues within 4Å: Chain D: F.52, A.53, V.56, W.57, R.60 Ligands: PC1.1 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.56 UND.10: 3 residues within 4Å: Chain E: P.29, I.32 Ligands: PC1.20 No protein-ligand interaction detected (PLIP) UND.11: 4 residues within 4Å: Chain E: L.30, L.34, K.37 Ligands: UND.17 No protein-ligand interaction detected (PLIP) UND.15: 3 residues within 4Å: Chain B: D.66 Chain G: Y.303, L.305 No protein-ligand interaction detected (PLIP) UND.16: 6 residues within 4Å: Chain C: V.35, R.39 Chain G: F.199, A.201, A.219, Y.221 No protein-ligand interaction detected (PLIP) UND.17: 9 residues within 4Å: Chain E: L.30, L.34 Chain G: Y.135, G.137, T.138, P.148, L.150, V.164 Ligands: UND.11 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.34 UND.19: 3 residues within 4Å: Chain H: F.92, V.96, V.100 No protein-ligand interaction detected (PLIP) UND.22: 4 residues within 4Å: Chain I: F.92, V.100, E.104 Ligands: PC1.21 No protein-ligand interaction detected (PLIP) UND.23: 4 residues within 4Å: Chain J: P.29, I.32, F.36 Ligands: PC1.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, D.S. et al., Tom core complex with Tom20 and Tom22 subunits. To Be Published

Release Date

2022-09-07

Peptides

Translocase of the Outer Membrane: AG
Mitochondrial import receptor subunit TOM6 homolog: BD
Mitochondrial import receptor subunit TOM5 homolog: CF
Mitochondrial import receptor subunit TOM7 homolog: EJ
Mitochondrial import receptor subunit TOM22 homolog: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
I

B
A

D
F

C
D

F
E

E
G

J
J

H
H

I
C

Membrane

We predict this structure to be a membrane protein.
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Translocase of the Outer Membrane

Mitochondrial import receptor subunit TOM6 homolog

Mitochondrial import receptor subunit TOM5 homolog

Mitochondrial import receptor subunit TOM7 homolog

Mitochondrial import receptor subunit TOM22 homolog

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