SMTL ID : 4z1m.1

Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-3-3-1-3-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.328, F.357, R.362, P.363, Q.430, Q.432 Chain D: Y.372 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432, A:Q.432 Water bridges: A:T.176, A:T.176, A:D.269 Salt bridges: A:K.175, A:K.175 ATP.4: 16 residues within 4Å: Chain B: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.328, F.357, R.362, Q.430, Q.432 Chain E: R.360, D.363 Ligands: MG.5 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:S.177, B:S.177, B:R.362, B:Q.430, E:R.360 Water bridges: B:K.175, B:T.176, B:D.269 Salt bridges: B:K.175, B:K.175, E:R.360, E:R.360 pi-Stacking: B:F.357 ATP.8: 17 residues within 4Å: Chain C: D.170, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, Q.430, G.431, Q.432 Chain F: R.360, M.362, D.363, Y.372 Ligands: MG.9 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:T.176, C:S.177, C:S.177, C:Q.430, C:Q.432, F:D.363 Water bridges: C:T.176 Salt bridges: C:K.175, C:K.175

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 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.5: 3 residues within 4Å: Chain B: T.176, D.269 Ligands: ATP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.176, H2O.1, H2O.1, H2O.1 MG.9: 3 residues within 4Å: Chain C: T.176, D.269 Ligands: ATP.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.176, H2O.1, H2O.1, H2O.1 MG.13: 2 residues within 4Å: Chain D: T.167 Ligands: ADP.12 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.167, H2O.1, H2O.1, H2O.1, H2O.1 MG.19: 2 residues within 4Å: Chain F: T.167 Ligands: ADP.18 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.167, H2O.1, H2O.1, H2O.1, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: E.50, M.62, V.129, G.130, Y.244, L.245, Y.248, R.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.304 GOL.7: 6 residues within 4Å: Chain B: M.62, V.129, G.130, Y.244, Y.248, R.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.244, B:R.304, B:R.304

11 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain B: A.114, P.120 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: S.123, R.126 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: G.130, Y.248, R.304 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: Q.215 Chain E: D.334 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: Q.225, N.227, E.228 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain E: E.245, R.248, D.249 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain E: Q.116, Y.246, Q.250 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain F: R.278, D.292 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain F: T.194, Q.225, N.227, E.228 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain F: V.283 Chain G: K.260, E.264 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain C: G.290 Chain D: P.280, G.284 Chain G: E.264 Ligand excluded by PLIP

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

ADP.12: 13 residues within 4Å: Chain C: R.373 Chain D: G.161, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, F.422, F.428, T.429 Ligands: MG.13 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:T.167, D:V.168 Water bridges: D:T.167, D:R.193, D:R.193, C:R.373, C:R.373 Salt bridges: D:K.166, C:R.373, C:R.373 pi-Stacking: D:Y.349, D:Y.349 ADP.18: 12 residues within 4Å: Chain B: R.373 Chain F: G.161, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, F.422, F.428 Ligands: MG.19 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:V.168, B:R.373, B:R.373 Water bridges: F:T.167, F:R.193, F:R.193, F:R.193, B:R.373 Salt bridges: F:K.166, B:R.373 pi-Stacking: F:Y.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bason, J.V. et al., How release of phosphate from mammalian F1-ATPase generates a rotary substep. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-05-06

Peptides

ATP synthase subunit alpha, mitochondrial: ABC
ATP synthase subunit beta, mitochondrial: DEF
ATP synthase subunit gamma, mitochondrial: G
ATPase inhibitor, mitochondrial: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATPase inhibitor, mitochondrial

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