SMTL ID : 7vby.1

Tom core complex with Tom20 and Tom22 subunits.

Coordinates

PDB Format Compare

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: 4 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:F.52, D:F.52, 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 Salt bridges: D:R.60, D:R.60 Hydrogen bonds: A:Y.254 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, 1 interactions with chain A, 2 interactions with chain J Salt bridges: H:R.82, H:R.82 Hydrophobic interactions: A:F.131, J:W.25, J:L.53 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 G, 3 interactions with chain B Hydrophobic interactions: G:V.299, G:F.301, B:A.54 Salt bridges: G:R.348, B:R.38, B:R.43 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: 7 interactions with chain G, 7 interactions with chain A, 4 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: 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, I:L.97, I:P.98 Salt bridges: G:K.330, A:K.330, A:K.330, H:K.105, I: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.
Show / Hide

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

Related Entries With Identical Sequence