SMTL ID : 7upr.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: D.72, I.73, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, Q.173, N.218, I.248, L.251, G.276 Chain D: M.197, D.201, A.226, R.229, R.230 Ligands: MG.2 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:A.74, A:A.74, A:G.116, A:G.118, A:K.119, A:T.120, A:T.120, A:L.121, A:Q.173, A:Q.173, D:D.201 Salt bridges: D:R.229, D:R.229, D:R.230, D:R.230 ATP.3: 20 residues within 4Å: Chain A: D.206, A.226, R.229, R.230 Chain B: D.72, I.73, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, Q.173, N.218, I.248, L.251, K.280 Ligands: MG.4 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:D.206, B:A.74, B:A.74, B:G.116, B:G.116, B:G.118, B:K.119, B:T.120, B:T.120, B:L.121, B:Q.173, B:Q.173, B:K.280, B:K.280 Salt bridges: A:R.229, A:R.229, A:R.230, A:R.230, B:K.119 ATP.5: 22 residues within 4Å: Chain C: D.72, I.73, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, Q.173, N.218, I.248, L.251, G.276, K.280 Chain E: D.201, D.206, A.226, R.229, R.230 Ligands: MG.6 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain E Hydrogen bonds: C:A.74, C:A.74, C:G.116, C:G.118, C:T.120, C:T.120, C:T.120, C:L.121, C:Q.173, E:D.206 Salt bridges: C:K.119, E:R.229, E:R.229, E:R.230, E:R.230 ATP.7: 22 residues within 4Å: Chain C: M.197, D.201, D.206, A.226, R.229, R.230 Chain D: D.72, I.73, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, Q.173, N.218, I.248, L.251, G.276 Ligands: MG.8 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:D.206, D:A.74, D:A.74, D:G.116, D:G.118, D:K.119, D:T.120, D:T.120, D:T.120, D:L.121, D:Q.173, D:Q.173 Salt bridges: C:R.229, C:R.229, C:R.230, C:R.230 ATP.9: 13 residues within 4Å: Chain E: D.72, A.74, P.115, G.116, C.117, G.118, K.119, T.120, L.121, D.172, I.248, S.277, K.280 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:A.74, E:A.74, E:G.116, E:G.118, E:K.119, E:T.120, E:D.172, E:D.172, E:K.280

4 x MG: MAGNESIUM ION(Non-covalent)

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

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
C

B
B

C
E

D
D

E
F

F
A

G
G

Outer mitochondrial transmembrane helix translocase

Unknown peptide substrate

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