SMTL ID : 8c0v.1

Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate in single seam state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: unknown peptide(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 9 residues within 4Å: Chain A: K.570 Chain B: Y.805, I.806, S.846 Chain C: K.570, I.572 Chain D: Y.805, I.806 Chain E: F.571 10 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C, 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: A:K.570, B:I.806, B:S.846, C:K.570, C:I.572 Hydrophobic interactions: B:Y.805, C:I.572, E:F.571, D:Y.805, D:I.806

10 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 10 residues within 4Å: Chain A: F.233, Q.263, G.264, G.266, K.267, T.268, R.269, P.442, L.443 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.263, A:G.264, A:G.266, A:T.268, A:T.268, A:R.269, A:R.269 Salt bridges: A:K.267 ATP.3: 18 residues within 4Å: Chain A: I.499, P.540, G.541, C.542, G.543, K.544, T.545, L.546, E.598, T.640, I.673, G.710, A.711, Q.714 Chain B: D.862, R.889, R.892 Ligands: MG.5 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.541, A:G.543, A:K.544, A:T.545, A:T.545, A:L.546, A:T.640 Salt bridges: A:K.544, A:K.544, B:R.889, B:R.889, B:R.889, B:R.892 ATP.6: 15 residues within 4Å: Chain B: F.444, Y.446, N.485, N.486, G.488, K.489, A.490, T.491, H.549, N.597, I.627, Y.631, P.667, K.671 Ligands: MG.8 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.486, B:G.488, B:K.489, B:A.490, B:T.491, B:Y.631 Salt bridges: B:K.489, B:K.489, B:H.549, C:K.391 ATP.7: 19 residues within 4Å: Chain B: D.733, I.734, I.737, P.774, G.775, T.776, G.777, K.778, T.779, L.780, Q.832, N.878, I.911, G.940, A.941, Y.944 Chain C: R.652, R.655 Ligands: MG.9 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:I.734, B:G.775, B:T.776, B:G.777, B:K.778, B:T.779, B:T.779, B:L.780, B:N.878, C:R.655 Salt bridges: B:K.778, C:R.652, C:R.652, C:R.655 ATP.10: 13 residues within 4Å: Chain C: F.233, I.234, V.236, Q.263, G.264, G.266, K.267, T.268, R.269, N.326, L.411, P.442 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:I.234, C:I.234, C:G.264, C:G.266, C:T.268, C:T.268, C:R.269, C:N.326 Salt bridges: C:K.267 ATP.11: 15 residues within 4Å: Chain C: D.498, P.540, G.541, C.542, G.543, K.544, T.545, L.546, I.673, A.711 Chain D: K.763, L.858, R.889, R.892 Ligands: MG.13 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:D.498, C:G.541, C:C.542, C:G.543, C:K.544, C:T.545, C:T.545, C:T.545, C:L.546, D:K.763, D:R.889 Salt bridges: C:K.544, C:K.544, D:R.889, D:R.889, D:R.892, D:R.892 ATP.14: 16 residues within 4Å: Chain D: F.444, Y.446, N.485, N.486, V.487, G.488, K.489, A.490, T.491, H.549, N.597, I.627, Y.631, P.667, K.671 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:N.485, D:N.486, D:V.487, D:G.488, D:K.489, D:A.490, D:T.491, D:T.491, D:N.597, D:Y.631, D:K.671 Salt bridges: D:K.489, D:H.549 ATP.15: 17 residues within 4Å: Chain D: D.733, I.734, G.735, G.775, T.776, G.777, K.778, T.779, L.780, I.911, G.940, A.941, Y.944 Chain E: D.626, R.652, R.655 Ligands: MG.17 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain D Hydrogen bonds: E:D.626, E:D.626, E:R.652, D:G.735, D:G.735, D:G.775, D:T.776, D:G.777, D:K.778, D:T.779, D:L.780 Salt bridges: E:R.655 ATP.18: 12 residues within 4Å: Chain E: F.233, I.234, Q.263, G.264, I.265, G.266, K.267, T.268, R.269, P.442, E.446 Ligands: MG.20 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:I.234, E:Q.263, E:G.264, E:G.266, E:G.266, E:K.267, E:T.268, E:R.269 Salt bridges: E:K.267 ATP.21: 15 residues within 4Å: Chain A: K.391 Chain F: F.444, Y.446, N.485, N.486, V.487, G.488, K.489, A.490, T.491, H.549, Y.631, L.668, K.671 Ligands: MG.23 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:Y.446, F:N.486, F:G.488, F:K.489, F:A.490, F:Y.631, F:K.671 Salt bridges: F:K.489, F:K.489, F:H.549, A:K.391, A:K.391

10 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: T.268 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.268 MG.5: 2 residues within 4Å: Chain A: T.545 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.545 MG.8: 2 residues within 4Å: Chain B: H.549 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: T.779, Q.832 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: T.268, D.325, N.326 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.268 MG.13: 2 residues within 4Å: Chain C: T.545 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.545 MG.16: 2 residues within 4Å: Chain D: H.549 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.549 MG.17: 3 residues within 4Å: Chain D: T.779 Chain E: D.626 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.626 MG.20: 2 residues within 4Å: Chain E: T.268 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.268 MG.23: 2 residues within 4Å: Chain F: H.549 Ligands: ATP.21 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.19: 9 residues within 4Å: Chain E: D.498, G.541, C.542, G.543, K.544, T.545, L.546, I.673, Q.714 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.498, E:G.543, E:K.544, E:T.545, E:L.546 ADP.22: 8 residues within 4Å: Chain F: P.774, G.775, T.776, G.777, K.778, T.779, L.780, Y.944 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.775, F:T.776, F:G.777, F:K.778, F:T.779, F:L.780, F:Y.944 Salt bridges: F:K.778, F:K.778 pi-Stacking: F:W.731, F:W.731

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruttermann, M. et al., Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nat Commun (2023)

Release Date

2023-10-04

Peptides

Peroxisomal ATPase PEX1: ACE
Peroxisomal ATPase PEX6: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Peroxisomal ATPase PEX1

Peroxisomal ATPase PEX6

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