SMTL ID : 1w0j.1

Beryllium fluoride inhibited bovine F1-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432 Chain D: Y.372 Ligands: MG.2 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432, D:Y.372 Water bridges: A:K.175, A:K.175, A:T.176, D:S.359, D:S.359, D:R.376, D:R.376 Salt bridges: A:K.175 ADP.4: 14 residues within 4Å: Chain B: D.170, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, Q.430, G.431, Q.432 Chain E: R.360, D.363 Ligands: MG.5 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:Q.172, B:T.173, B:T.173, B:G.174, B:K.175, B:T.176, B:T.176, B:S.177, B:S.177, B:Q.430, E:R.360, E:R.360, E:D.363 Water bridges: B:K.175, B:K.175, B:K.175, B:T.176, E:R.360 Salt bridges: B:K.175 ADP.7: 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.8 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:S.177, C:Q.430, C:Q.432, F:Y.372 Water bridges: C:K.175, C:K.175, C:T.176, C:Q.432 Salt bridges: C:K.175 ADP.11: 17 residues within 4Å: Chain C: S.372, R.373 Chain D: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, F.422, A.425, F.428, T.429 Ligands: MG.12, BEF.13 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.161, D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:V.168, C:S.372 Water bridges: D:T.167, D:L.169, D:R.193, D:D.260, D:Q.420, C:R.373 Salt bridges: D:K.166, C:R.373, C:R.373 pi-Stacking: D:Y.349, D:Y.349 ADP.15: 16 residues within 4Å: Chain B: V.371, R.373 Chain F: 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.16, BEF.17 19 PLIP interactions: 16 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.161, F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:V.168 Water bridges: F:T.167, F:L.169, F:R.193, F:E.196, F:D.260, F:Q.420, B:R.373 Salt bridges: F:K.166, B:R.373, B:R.373 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 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.176, H2O.3, H2O.4, H2O.7, H2O.7 MG.5: 2 residues within 4Å: Chain B: T.176 Ligands: ADP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.176, H2O.10, H2O.10, H2O.13, H2O.13 MG.8: 2 residues within 4Å: Chain C: T.176 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.176, H2O.16, H2O.16, H2O.17, H2O.21 MG.12: 6 residues within 4Å: Chain D: T.167, E.192, R.193, D.260 Ligands: ADP.11, BEF.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.167, H2O.23, H2O.24, H2O.25 MG.16: 4 residues within 4Å: Chain F: T.167, R.193 Ligands: ADP.15, BEF.17 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.167, H2O.35, H2O.36, H2O.39

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: M.62, G.130, Y.244, L.245, Y.248, R.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.244, A:R.304, A:R.304 Water bridges: A:L.131, A:R.308 GOL.6: 5 residues within 4Å: Chain B: V.129, G.130, Y.244, Y.248, R.304 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.244, B:R.304, B:R.304 Water bridges: B:V.129, B:G.130, B:R.304, B:R.304 GOL.9: 7 residues within 4Å: Chain C: M.62, V.129, G.130, Y.244, L.245, Y.248, R.304 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.244, C:Y.244, C:R.304 Water bridges: C:G.130, C:R.304 GOL.10: 5 residues within 4Å: Chain D: R.235, G.269, R.278, Q.286, D.292 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.235, D:S.273, D:R.278, D:R.278 Water bridges: D:G.269

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.13: 11 residues within 4Å: Chain C: I.343, S.344, R.373 Chain D: A.162, G.163, K.166, E.192, R.193, Y.315 Ligands: ADP.11, MG.12 No protein-ligand interaction detected (PLIP) BEF.17: 12 residues within 4Å: Chain B: I.343, S.344, R.373 Chain F: A.162, G.163, K.166, T.167, E.192, R.193, Y.315 Ligands: ADP.15, MG.16 No protein-ligand interaction detected (PLIP)

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

PO4.14: 6 residues within 4Å: Chain E: A.162, G.163, V.164, G.165, K.166, T.167 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.163, E:G.165, E:K.166, E:T.167, E:T.167 Water bridges: E:V.164, E:V.164, E:T.167, E:V.168

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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