SMTL ID : 6q45.2 (1 other biounit)

F1-ATPase from Fusobacterium nucleatum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, A.177, F.349, R.354, P.355, Q.422, P.423, Q.424 Chain D: K.343, Y.355 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.172, A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:A.177, A:Q.422, A:Q.424 Water bridges: A:T.176 Salt bridges: A:K.175, A:K.175 ATP.3: 16 residues within 4Å: Chain B: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, A.177, E.320, F.349, R.354, P.355, Q.422, P.423, Q.424 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.170, B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:A.177, B:E.320, B:E.320, B:R.354, B:Q.422 Water bridges: B:T.176 Salt bridges: B:K.175, B:K.175 ATP.5: 16 residues within 4Å: Chain C: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, A.177, E.320, F.349, R.354, P.355, Q.422, P.423, Q.424 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:T.176, C:A.177, C:E.320, C:E.320, C:Q.422, C:Q.424 Water bridges: C:K.175, C:K.175, C:T.176 Salt bridges: C:K.175, C:K.175

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.176, D.261 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.176, H2O.1, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: T.176 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.176, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain C: T.176, D.261 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.176, H2O.1, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain D: T.156, R.182 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.156, H2O.1, H2O.1, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain F: T.156, R.182, E.185 Ligands: ADP.9 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.156, H2O.1, H2O.1, H2O.1, H2O.1

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

ADP.7: 16 residues within 4Å: Chain C: V.363, S.364, R.365 Chain D: G.150, A.151, G.152, V.153, G.154, K.155, T.156, V.157, Y.332, F.405, A.408, F.411 Ligands: MG.8 17 PLIP interactions: 3 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:S.364, D:G.152, D:V.153, D:G.154, D:K.155, D:T.156, D:V.157 Salt bridges: C:R.365, C:R.365, D:K.155 Water bridges: D:K.155, D:R.182, D:R.182, D:R.182, D:R.182, D:D.243 pi-Stacking: D:Y.332 ADP.9: 12 residues within 4Å: Chain B: R.365 Chain F: G.150, G.152, V.153, G.154, K.155, T.156, V.157, Y.332, F.405, F.411 Ligands: MG.10 16 PLIP interactions: 2 interactions with chain B, 14 interactions with chain F Hydrogen bonds: B:R.365, F:G.150, F:G.152, F:V.153, F:G.154, F:K.155, F:T.156, F:V.157 Salt bridges: B:R.365, F:K.155 Water bridges: F:R.182, F:R.182, F:R.182, F:R.182 pi-Stacking: F:Y.332, F:Y.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petri, J. et al., Structure of F1-ATPase from the obligate anaerobe Fusobacterium nucleatum. Open Biology (2019)

Release Date

2019-07-10

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

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