SMTL ID : 8c0w.1

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

Coordinates

PDB Format Compare

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: M.804, Y.805 Chain B: F.571 Chain C: M.804, Y.805, I.806, S.846 Chain D: K.570, I.572 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:M.804, C:I.806, C:S.846 Hydrophobic interactions: D:I.572

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

ATP.2: 15 residues within 4Å: Chain A: F.444, Y.446, N.485, N.486, V.487, G.488, K.489, A.490, T.491, H.549, I.627, Y.631, P.667, L.668 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.486, A:V.487, A:G.488, A:G.488, A:K.489, A:A.490, A:T.491, A:T.491, A:Y.631 Salt bridges: A:K.489, A:K.489 ATP.3: 20 residues within 4Å: Chain A: D.733, I.734, G.735, P.774, G.775, T.776, G.777, K.778, T.779, L.780, D.831, Q.832, N.878, I.911, L.915, G.940, A.941, Y.944 Chain B: R.655 Ligands: MG.5 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.735, A:G.735, A:G.775, A:G.777, A:K.778, A:T.779, A:D.831, A:Q.832, A:G.940 Salt bridges: A:K.778, B:R.655, B:R.655, B:R.655 ATP.6: 14 residues within 4Å: Chain B: F.233, I.234, V.236, Q.263, G.264, G.266, K.267, T.268, R.269, N.326, F.415, P.442, L.443 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.234, B:G.264, B:G.266, B:K.267, B:T.268, B:T.268, B:T.268, B:R.269, B:N.326 ATP.7: 13 residues within 4Å: Chain B: G.541, C.542, G.543, T.545, L.546, I.673, G.710, A.711, Q.714 Chain C: D.862, P.890, R.892 Ligands: MG.9 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain B Salt bridges: C:R.892 Hydrogen bonds: B:C.542, B:C.542, B:T.545, B:T.545, B:L.546, B:G.710, B:A.711, B:Q.714 ATP.10: 13 residues within 4Å: Chain C: F.444, Y.446, N.486, V.487, G.488, K.489, A.490, T.491, H.549, N.597, Y.631, P.667 Ligands: MG.12 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.486, C:N.486, C:A.490, C:T.491, C:N.597 Salt bridges: C:K.489, C:H.549, D:K.391 ATP.11: 14 residues within 4Å: Chain C: D.733, I.734, G.735, P.774, G.775, T.776, G.777, K.778, T.779, L.780, A.941, Y.944 Chain D: R.529 Ligands: MG.13 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.735, C:G.735, C:G.775, C:T.776, C:G.777, C:K.778, C:T.779, C:T.779, C:L.780, D:R.529 Salt bridges: C:K.778, C:K.778 ATP.14: 14 residues within 4Å: Chain D: F.233, I.234, V.236, Q.263, G.264, I.265, G.266, K.267, T.268, R.269, N.326, P.442, E.446 Ligands: MG.16 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:I.234, D:Q.263, D:G.264, D:I.265, D:K.267, D:T.268, D:R.269, D:R.269, D:R.269 Salt bridges: D:K.267 ATP.17: 13 residues within 4Å: Chain E: F.444, N.485, N.486, V.487, G.488, K.489, A.490, T.491, H.549, I.627, L.668 Chain F: K.391 Ligands: MG.19 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.488, E:A.490, E:T.491, E:T.491, E:T.491 Salt bridges: E:K.489, E:H.549, F:K.391 pi-Stacking: E:F.444 ATP.18: 14 residues within 4Å: Chain E: W.731, G.775, T.776, G.777, K.778, T.779, L.780, Q.832, A.941, Y.944 Chain F: R.529, R.652, R.655 Ligands: MG.20 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:R.529, E:G.777, E:K.778, E:T.779, E:Q.832 Salt bridges: F:R.652, F:R.652, F:R.655, F:R.655 ATP.21: 13 residues within 4Å: Chain F: F.233, I.234, Q.263, G.264, I.265, G.266, K.267, T.268, R.269, D.325, L.411, P.442 Ligands: MG.23 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:Q.263, F:G.264, F:G.266, F:K.267, F:T.268, F:T.268, F:R.269, F:R.269

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 2 residues within 4Å: Chain A: H.549 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.549 MG.5: 4 residues within 4Å: Chain A: T.779, D.831, Q.832 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.779, A:D.831, A:D.831 MG.8: 2 residues within 4Å: Chain B: T.268 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.268 MG.9: 3 residues within 4Å: Chain B: C.542, T.545 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.542, B:T.545 MG.12: 1 residues within 4Å: Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain C: T.779 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.779 MG.16: 2 residues within 4Å: Chain D: T.268 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.268 MG.19: 1 residues within 4Å: Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain E: T.779 Chain F: R.655 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.779 MG.23: 2 residues within 4Å: Chain F: T.268 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.268

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

ADP.15: 11 residues within 4Å: Chain D: G.500, A.501, G.541, C.542, G.543, K.544, T.545, L.546, G.710, D.712, Q.714 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.501, D:G.543, D:T.545, D:T.545, D:D.712, D:Q.714 ADP.22: 9 residues within 4Å: Chain F: G.500, G.541, C.542, G.543, K.544, T.545, L.546, I.673, L.713 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.541, F:C.542, F:K.544, F:T.545 Salt bridges: F:K.544, F:K.544

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 PEX6: ACE
Peroxisomal ATPase PEX1: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Peroxisomal ATPase PEX6

Peroxisomal ATPase PEX1

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