SMTL ID : 7upt.1

Human mitochondrial AAA protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate (open conformation)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.1: 14 residues within 4Å: Chain A: D.72, I.73, A.74, G.75, L.76, G.116, T.120, L.121, Q.244, I.248, L.251, G.276, S.277, K.280 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.72, A:A.74, A:L.76, A:C.117, A:T.120, A:Q.244 Salt bridges: A:K.280, A:K.280

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.120, D.172 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.120 MG.4: 4 residues within 4Å: Chain B: R.230 Chain C: T.120, D.172 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.120 MG.7: 3 residues within 4Å: Chain A: D.201 Chain D: T.120 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.120 MG.9: 4 residues within 4Å: Chain E: T.120, D.172, Q.173 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.120, E:D.172 MG.10: 3 residues within 4Å: Chain F: T.120, D.172 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.120

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

ATP.3: 19 residues within 4Å: Chain B: D.72, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, D.172, Q.173, N.218, I.248, K.280 Chain D: D.201, D.206, R.229, R.230 Ligands: MG.2 16 PLIP interactions: 5 interactions with chain D, 11 interactions with chain B Hydrogen bonds: D:D.206, B:A.74, B:A.74, B:G.116, B:G.116, B:G.118, B:K.119, B:T.120, B:L.121, B:N.218, B:N.218, B:K.280 Salt bridges: D:R.229, D:R.229, D:R.230, D:R.230 ATP.5: 18 residues within 4Å: Chain B: D.206, R.229, R.230 Chain C: D.72, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, D.172, Q.173, I.248, L.251, S.277 Ligands: MG.4 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:A.74, C:A.74, C:G.116, C:G.116, C:G.118, C:K.119, C:T.120, C:L.121, C:Q.173, B:D.206 Salt bridges: B:R.229, B:R.229, B:R.230, B:R.230 ATP.6: 18 residues within 4Å: Chain A: D.201, T.205, R.229, R.230 Chain D: D.72, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, Q.173, A.216, I.248, S.277 Ligands: MG.7 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:A.74, D:A.74, D:G.116, D:G.116, D:G.118, D:K.119, D:T.120, D:L.121, D:Q.173, D:A.216 Salt bridges: A:R.229, A:R.229, A:R.230, A:R.230 ATP.8: 19 residues within 4Å: Chain C: D.201, R.229, R.230 Chain E: D.72, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, D.172, Q.173, I.248, L.251, S.277, K.280 Ligands: MG.9 15 PLIP interactions: 5 interactions with chain C, 10 interactions with chain E Hydrogen bonds: C:D.206, E:A.74, E:A.74, E:G.116, E:G.116, E:G.118, E:K.119, E:T.120, E:L.121, E:Q.173, E:Q.173 Salt bridges: C:R.229, C:R.229, C:R.229, C:R.230 ATP.11: 18 residues within 4Å: Chain E: R.229, R.230 Chain F: D.72, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, D.172, Q.173, I.248, L.251, S.277, K.280 Ligands: MG.10 14 PLIP interactions: 9 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:A.74, F:A.74, F:G.116, F:G.116, F:G.118, F:K.119, F:T.120, F:L.121, F:Q.173 Salt bridges: E:R.229, E:R.229, E:R.229, E:R.230, E:R.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Conserved structural elements specialize ATAD1 as a membrane protein extraction machine. Elife (2022)

Release Date

2022-06-15

Peptides

Outer mitochondrial transmembrane helix translocase: ABCDEF
Unknown peptide substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Outer mitochondrial transmembrane helix translocase

Unknown peptide substrate

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