SMTL ID : 8u0v.1

S. cerevisiae Pex1/Pex6 with 1 mM ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: I.699, A.701, L.702, P.740, G.741, C.742, G.743, K.744, T.745, L.746, S.841, I.873, G.910, A.911, Q.914 Chain E: R.903 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:G.741, A:C.742, A:G.743, A:K.744, A:T.745, A:T.745, A:T.745, A:S.841, A:G.910, A:Q.914 Salt bridges: A:K.744, A:K.744, E:R.903, E:R.903 ATP.2: 14 residues within 4Å: Chain A: D.429, D.431, Q.463, G.464, I.465, G.466, K.467, T.468, R.469, D.525, F.615, P.642, L.643, E.646 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.431, A:G.464, A:I.465, A:G.466, A:K.467, A:T.468, A:R.469, A:R.469, A:R.469 Salt bridges: A:K.467, A:K.467 pi-Cation interactions: A:R.469 ATP.3: 15 residues within 4Å: Chain B: D.431, F.433, K.462, Q.463, G.464, I.465, G.466, K.467, T.468, R.469, L.611, F.615, P.642, L.643, E.646 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.431, B:D.431, B:K.462, B:Q.463, B:G.464, B:I.465, B:G.466, B:T.468, B:T.468, B:T.468, B:R.469, B:R.469 Salt bridges: B:K.467, B:K.467 ATP.4: 19 residues within 4Å: Chain B: I.699, G.700, A.701, L.702, Y.739, P.740, G.741, C.742, G.743, K.744, T.745, L.746, L.747, I.873, G.910, Q.914 Chain F: D.876, R.903, R.906 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:G.700, B:G.700, B:Y.739, B:G.741, B:C.742, B:G.743, B:K.744, B:T.745, B:T.745, B:T.745, B:L.746, B:Q.914 Salt bridges: B:K.744, B:K.744, F:R.903, F:R.906, F:R.906, F:R.906 ATP.5: 16 residues within 4Å: Chain C: D.431, F.433, V.436, I.465, G.466, K.467, T.468, R.469, L.470, K.579, L.611, F.615, P.642, L.643, E.646 Chain D: H.623 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.431, C:D.431, C:T.468, C:T.468, C:R.469 Salt bridges: C:R.469, D:H.623 pi-Stacking: C:F.433 ATP.6: 14 residues within 4Å: Chain A: K.591 Chain D: F.458, N.499, N.500, V.501, G.502, K.503, A.504, T.505, H.563, I.641, Y.645, P.681, L.682 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.500, D:V.501, D:G.502, D:K.503, D:A.504, D:T.505, D:T.505 Salt bridges: D:K.503, D:K.503, D:H.563, A:K.591 ATP.7: 16 residues within 4Å: Chain B: K.591 Chain E: F.458, Y.460, N.499, N.500, V.501, G.502, K.503, A.504, T.505, H.563, I.641, Y.645, P.681, L.682, K.685 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:Y.460, E:N.499, E:N.500, E:G.502, E:K.503, E:A.504, E:T.505, E:T.505, E:Y.645, E:K.685 Salt bridges: E:K.503, E:K.503, E:H.563, B:K.591 ATP.8: 19 residues within 4Å: Chain B: L.822, D.826, R.852, R.855 Chain E: I.748, G.749, I.751, G.789, T.790, G.791, K.792, T.793, L.794, E.846, I.925, L.929, G.954, A.955, Y.958 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain B Hydrogen bonds: E:G.749, E:G.749, E:G.789, E:T.790, E:G.791, E:K.792, E:T.793, E:T.793, E:T.793, E:L.794, E:E.846 Salt bridges: E:K.792, E:K.792, B:R.852, B:R.852, B:R.855, B:R.855, B:R.855 ATP.9: 15 residues within 4Å: Chain C: K.591 Chain F: F.458, Y.460, N.499, N.500, V.501, G.502, K.503, A.504, T.505, H.563, I.641, Y.645, P.681, L.682 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:Y.460, F:N.500, F:V.501, F:G.502, F:K.503, F:A.504, F:T.505, F:T.505 Salt bridges: F:K.503, F:K.503, F:H.563 ATP.10: 19 residues within 4Å: Chain C: D.826, R.852, P.853, R.855 Chain F: I.748, G.749, P.788, G.789, T.790, G.791, K.792, T.793, L.794, N.892, I.925, L.929, G.954, A.955, Y.958 19 PLIP interactions: 13 interactions with chain F, 6 interactions with chain C Hydrogen bonds: F:G.749, F:G.749, F:G.789, F:T.790, F:T.790, F:G.791, F:K.792, F:T.793, F:T.793, F:T.793, F:L.794, C:P.853 Salt bridges: F:K.792, F:K.792, C:R.852, C:R.852, C:R.852, C:R.855, C:R.855

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ali, B.A. et al., The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1. J.Biol.Chem. (2023)

Release Date

2023-12-13

Peptides

Peroxisomal ATPase PEX1: ABC
Peroxisomal ATPase PEX6: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
F

E
B

F
D

Peroxisomal ATPase PEX1

Peroxisomal ATPase PEX6