SMTL ID : 4yxw.1

Bovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP in the presence of thiophosphate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-3-3-1-1-1-mer

Ligands

5 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 17 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: S.359, Y.372 Ligands: MG.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:Q.172, A:Q.172, A:T.173, A:G.174, A:K.175, A:K.175, A:K.175, A:T.176, A:S.177, A:S.177, A:E.328, A:E.328, A:Q.430, A:Q.432, A:Q.432, A:Y.433, D:S.359, D:Y.372, D:R.376 Water bridges: A:T.176, A:T.176, A:T.176 ANP.3: 16 residues within 4Å: Chain B: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain E: R.360, D.363 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.172, B:Q.172, B:T.173, B:G.174, B:K.175, B:K.175, B:K.175, B:T.176, B:S.177, B:S.177, B:R.362, B:Q.430, B:Q.432 ANP.5: 14 residues within 4Å: Chain C: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain F: Y.372 Ligands: MG.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:K.175, C:K.175, C:T.176, C:S.177, C:S.177, C:Q.430, F:S.359, F:Y.372 ANP.7: 21 residues within 4Å: Chain C: S.344, V.371, S.372, R.373 Chain D: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, Y.315, Y.349, F.422, A.425, F.428, T.429 Ligands: MG.8 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.163, D:V.164, D:G.165, D:K.166, D:K.166, D:K.166, D:T.167, D:V.168, D:R.193, D:R.193, D:Y.349, C:S.344, C:S.372, C:R.373, C:R.373 Water bridges: D:E.192, D:N.261 pi-Stacking: D:Y.349, D:Y.349 Salt bridges: C:R.373 ANP.11: 21 residues within 4Å: Chain B: I.343, S.344, V.371, R.373 Chain F: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, Y.315, Y.349, F.422, A.425, F.428, T.429 Ligands: MG.12 22 PLIP interactions: 18 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.163, F:V.164, F:G.165, F:K.166, F:K.166, F:K.166, F:T.167, F:V.168, F:R.193, F:R.193, B:S.344, B:R.373, B:R.373 Water bridges: F:K.166, F:T.167, F:T.167, F:T.167, F:N.261, F:Q.420 pi-Stacking: F:Y.349, F:Y.349 Salt bridges: B:R.373

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.176, D.269 Ligands: ANP.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: 3 residues within 4Å: Chain B: T.176, D.269 Ligands: ANP.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.269 Ligands: ANP.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.167, D.260 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.167, H2O.1, H2O.1, H2O.1 MG.12: 3 residues within 4Å: Chain F: T.167, R.193 Ligands: ANP.11 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.167, H2O.2, H2O.2, H2O.2

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

CL.9: 4 residues within 4Å: Chain D: V.367, G.368, E.370, H.371 Ligand excluded by PLIP

1 x TS6: Monothiophosphate(Non-covalent)

TS6.10: 5 residues within 4Å: Chain E: K.166, R.193, D.260, N.261, R.264 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.193, E:N.261, E:R.264, E:R.264

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 6 residues within 4Å: Chain F: I.141, K.142, V.143, P.350, L.418, Q.420 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.142, F:V.143, F:Q.420

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
ATP synthase subunit delta, mitochondrial: H
ATP synthase subunit epsilon, mitochondrial: I

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

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial