SMTL ID : 2f43.1

Rat liver F1-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-3-3-1-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.176, Q.208, D.269 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.176 MG.4: 6 residues within 4Å: Chain B: T.163, E.188, R.189, D.256 Ligands: VO4.3, ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.163 MG.6: 4 residues within 4Å: Chain C: T.176, Q.208, D.269 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.9: 6 residues within 4Å: Chain D: T.163, E.188, R.189, D.256 Ligands: VO4.8, ADP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.163 MG.11: 4 residues within 4Å: Chain E: T.176, Q.208, D.269 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.176 MG.14: 6 residues within 4Å: Chain F: T.163, E.188, R.189, D.256 Ligands: VO4.13, ADP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.163

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

ATP.2: 14 residues within 4Å: Chain A: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, G.431, Q.432 Chain B: S.355, D.359 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.170, A:Q.172, A:Q.172, A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:Q.432 Salt bridges: A:K.175, A:K.175 ATP.7: 14 residues within 4Å: Chain C: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, G.431, Q.432 Chain D: S.355, D.359 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.170, C:Q.172, C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:Q.432 Salt bridges: C:K.175, C:K.175 ATP.12: 14 residues within 4Å: Chain E: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, G.431, Q.432 Chain F: S.355, D.359 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.170, E:Q.172, E:Q.172, E:Q.172, E:T.173, E:G.174, E:K.175, E:T.176, E:S.177, E:Q.432 Salt bridges: E:K.175, E:K.175

3 x VO4: VANADATE ION(Non-covalent)

VO4.3: 11 residues within 4Å: Chain B: A.158, G.159, K.162, E.188, R.189, N.257, Y.311 Chain C: S.344, R.373 Ligands: MG.4, ADP.5 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.158, B:G.159, B:K.162, B:R.189, B:R.189, B:N.257, B:R.260, C:R.373 VO4.8: 11 residues within 4Å: Chain D: A.158, G.159, K.162, E.188, R.189, N.257, Y.311 Chain E: S.344, R.373 Ligands: MG.9, ADP.10 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.158, D:G.159, D:K.162, D:R.189, D:R.189, D:N.257, D:R.260, E:R.373 VO4.13: 11 residues within 4Å: Chain A: S.344, R.373 Chain F: A.158, G.159, K.162, E.188, R.189, N.257, Y.311 Ligands: MG.14, ADP.15 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:A.158, F:G.159, F:K.162, F:R.189, F:R.189, F:N.257, F:R.260, A:R.373

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

ADP.5: 15 residues within 4Å: Chain B: G.159, V.160, G.161, K.162, T.163, V.164, R.189, Y.345, F.418, A.421, F.424 Chain C: V.371, R.373 Ligands: VO4.3, MG.4 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.159, B:V.160, B:G.161, B:K.162, B:T.163, B:T.163, B:T.163, B:V.164, C:R.373 Salt bridges: B:K.162, B:R.189, C:R.373, C:R.373 pi-Stacking: B:Y.345, B:Y.345 ADP.10: 15 residues within 4Å: Chain D: G.159, V.160, G.161, K.162, T.163, V.164, R.189, Y.345, F.418, A.421, F.424 Chain E: V.371, R.373 Ligands: VO4.8, MG.9 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.159, D:V.160, D:G.161, D:K.162, D:T.163, D:T.163, D:T.163, D:V.164, E:R.373 Salt bridges: D:K.162, D:R.189, E:R.373, E:R.373 pi-Stacking: D:Y.345, D:Y.345 ADP.15: 15 residues within 4Å: Chain A: V.371, R.373 Chain F: G.159, V.160, G.161, K.162, T.163, V.164, R.189, Y.345, F.418, A.421, F.424 Ligands: VO4.13, MG.14 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.159, F:V.160, F:G.161, F:K.162, F:T.163, F:T.163, F:T.163, F:V.164, A:R.373 Salt bridges: F:K.162, F:R.189, A:R.373, A:R.373 pi-Stacking: F:Y.345, F:Y.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C. et al., Mitochondrial ATP synthase: Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism. J.Biol.Chem. (2006)

Release Date

2006-03-07

Peptides

ATP synthase alpha chain, mitochondrial: ACE
ATP synthase beta chain, mitochondrial: BDF
ATP synthase gamma chain, mitochondrial: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

G
G

ATP synthase alpha chain, mitochondrial

ATP synthase beta chain, mitochondrial

ATP synthase gamma chain, mitochondrial

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