SMTL ID : 1w0k.1

ADP inhibited bovine F1-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-3-3-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, Q.430, Q.432 Chain D: Y.372 Ligands: MG.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D 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, D:S.359 Salt bridges: A:K.175 pi-Stacking: A:F.357 ADP.3: 14 residues within 4Å: Chain B: D.170, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain E: D.363 Ligands: MG.4 10 PLIP interactions: 9 interactions with chain B, 1 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:Q.430, E:D.363 Salt bridges: B:K.175 ADP.6: 16 residues within 4Å: Chain C: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, G.431, Q.432 Chain F: Y.372 Ligands: MG.7 13 PLIP interactions: 13 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:S.177, C:S.177, C:Q.430, C:Q.432 Salt bridges: C:K.175 pi-Stacking: C:F.357 ADP.9: 16 residues within 4Å: Chain C: V.371, S.372, R.373 Chain D: G.161, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, F.422, A.425, F.428, T.429 Ligands: MG.10 16 PLIP interactions: 4 interactions with chain C, 12 interactions with chain D Hydrogen bonds: C:S.372, D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:V.168, D:Y.349 Water bridges: C:R.373, D:K.166, D:K.166 Salt bridges: C:R.373, C:R.373, D:K.166 pi-Stacking: D:Y.349, D:Y.349 ADP.13: 12 residues within 4Å: Chain B: V.371, R.373 Chain F: G.163, V.164, G.165, K.166, T.167, V.168, Y.349, F.422, F.428 Ligands: MG.14 11 PLIP interactions: 9 interactions with chain F, 2 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 Salt bridges: F:K.166 pi-Stacking: F:Y.349, F:Y.349

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.176 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.176, H2O.2 MG.4: 2 residues within 4Å: Chain B: T.176 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.176 MG.7: 2 residues within 4Å: Chain C: T.176 Ligands: ADP.6 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.176, H2O.5 MG.10: 5 residues within 4Å: Chain D: T.167, E.192, R.193, D.260 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.167 MG.14: 5 residues within 4Å: Chain F: T.167, E.192, R.193, E.196 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.167

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: M.62, V.129, G.130, Y.244, L.245, Y.248, R.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.244, B:R.304, B:R.304 GOL.8: 7 residues within 4Å: Chain C: E.50, M.62, V.129, G.130, Y.244, Y.248, R.304 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.50, C:E.50, C:R.304, C:R.304 GOL.11: 5 residues within 4Å: Chain D: R.235, G.269, R.278, Q.286, D.292 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.235, D:R.278, D:R.278, D:Q.286, D:T.288, D:T.288

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

PO4.12: 6 residues within 4Å: Chain E: A.162, G.163, V.164, G.165, K.166, T.167 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.163, E:V.164, E:K.166, E:T.167, E:T.167, E:T.167, E:T.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kagawa, R. et al., The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride. Embo J. (2004)

Release Date

2004-07-08

Peptides

ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOCHONDRIAL PRECURSOR: ABC
ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR: DEF
ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP SYNTHASE ALPHA CHAIN HEART ISOFORM, MITOCHONDRIAL PRECURSOR

ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR

ATP SYNTHASE GAMMA CHAIN, MITOCHONDRIAL PRECURSOR

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