SMTL ID : 1mab.1

RAT LIVER F1-ATPASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-3-3-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.176 Ligands: ATP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.176, H2O.2 MG.5: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.6 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.176, H2O.4 MG.9: 2 residues within 4Å: Chain E: T.176 Ligands: ATP.10 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.176, H2O.6

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

ATP.2: 14 residues within 4Å: Chain A: D.170, 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: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.172, A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:R.362, A:Q.432, B:S.355 Water bridges: A:T.176 Salt bridges: A:K.175 ATP.6: 14 residues within 4Å: Chain C: D.170, 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.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:R.362, C:Q.432, D:S.355 Water bridges: C:T.176 Salt bridges: C:K.175 ATP.10: 14 residues within 4Å: Chain E: D.170, 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.9 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Q.172, E:Q.172, E:T.173, E:G.174, E:K.175, E:T.176, E:S.177, E:R.362, E:Q.432, F:S.355 Water bridges: E:T.176 Salt bridges: E:K.175

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain B: G.159, K.162, T.163, E.188, R.189, N.257 Chain C: S.344, R.373 Ligands: ADP.4 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:R.373, B:G.159, B:T.163, B:E.188, B:E.188, B:D.256, B:N.257 Salt bridges: B:K.162, B:R.189 PO4.7: 9 residues within 4Å: Chain D: G.159, K.162, T.163, E.188, R.189, N.257 Chain E: S.344, R.373 Ligands: ADP.8 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.159, D:T.163, D:E.188, D:E.188, D:D.256, D:N.257, E:R.373 Salt bridges: D:K.162, D:R.189 PO4.11: 9 residues within 4Å: Chain A: S.344, R.373 Chain F: G.159, K.162, T.163, E.188, R.189, N.257 Ligands: ADP.12 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.159, F:T.163, F:E.188, F:E.188, F:D.256, F:N.257, A:R.373 Salt bridges: F:K.162, F:R.189

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

ADP.4: 15 residues within 4Å: Chain B: G.159, V.160, G.161, K.162, T.163, V.164, R.189, Y.345, P.417, F.418, A.421, F.424 Chain C: V.371, R.373 Ligands: PO4.3 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:R.373, B:G.159, B:V.160, B:G.161, B:K.162, B:T.163, B:T.163, B:V.164, B:Y.345, B:P.417 Salt bridges: C:R.373, C:R.373, B:K.162, B:R.189 pi-Stacking: B:Y.345 ADP.8: 15 residues within 4Å: Chain D: G.159, V.160, G.161, K.162, T.163, V.164, R.189, Y.345, P.417, F.418, A.421, F.424 Chain E: V.371, R.373 Ligands: PO4.7 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:V.164, D:Y.345, D:P.417, E:R.373 Salt bridges: D:K.162, D:R.189, E:R.373, E:R.373 pi-Stacking: D:Y.345 ADP.12: 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, P.417, F.418, A.421, F.424 Ligands: PO4.11 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:V.164, F:Y.345, F:P.417, A:R.373 Salt bridges: F:K.162, F:R.189, A:R.373, A:R.373 pi-Stacking: F:Y.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bianchet, M.A. et al., The 2.8-A structure of rat liver F1-ATPase: configuration of a critical intermediate in ATP synthesis/hydrolysis. Proc.Natl.Acad.Sci.USA (1998)

Release Date

1998-09-30

Peptides

PROTEIN (F1-ATPASE ALPHA CHAIN): ACE
PROTEIN (F1-ATPASE BETA CHAIN): BDF
PROTEIN (F1-ATPASE GAMMA CHAIN): G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

G
G

PROTEIN (F1-ATPASE ALPHA CHAIN)

PROTEIN (F1-ATPASE BETA CHAIN)

PROTEIN (F1-ATPASE GAMMA CHAIN)

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