SMTL ID : 2jj1.2 (1 other biounit)

The Structure of F1-ATPase inhibited by piceatannol.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-3-3-1-mer

Ligands

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

ANP.1: 15 residues within 4Å: Chain A: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, P.363, Q.430, Q.432, Y.433 Chain D: Y.372 Ligands: MG.2 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:K.175, A:T.176, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432, A:Y.433, A:Y.433, D:Y.372 Water bridges: A:Q.172, A:Q.172, A:Q.172, A:K.175, A:T.176, A:D.270, A:E.328, A:Q.430 ANP.5: 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, Q.430, G.431, Q.432 Chain E: R.360, D.363 Ligands: MG.6 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 Water bridges: B:T.176 ANP.8: 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.9 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:K.175, C:T.176, C:S.177, C:S.177, C:Q.430, C:Q.432, F:Y.372 Water bridges: C:T.176, C:T.176, C:T.176, C:T.176 ANP.17: 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.18 23 PLIP interactions: 19 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:T.167, F:V.168, F:E.192, F:R.193, F:R.193, B:R.373, B:R.373 Water bridges: F:K.166, F:T.167, F:T.167, F:T.167, F:E.192, F:E.192, F:D.260, B:S.344 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.2, H2O.3, H2O.3 MG.6: 2 residues within 4Å: Chain B: T.176 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.176, H2O.5, H2O.5, H2O.7 MG.9: 2 residues within 4Å: Chain C: T.176 Ligands: ANP.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.176, H2O.8, H2O.11, H2O.11 MG.12: 5 residues within 4Å: Chain D: T.167, E.192, R.193, D.260 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.167, H2O.12, H2O.12, H2O.13, H2O.14 MG.18: 6 residues within 4Å: Chain F: T.167, E.192, R.193, E.196, D.260 Ligands: ANP.17 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.167, H2O.19, H2O.21, H2O.21

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.50, M.62, G.130, Y.244, L.245, Y.248, R.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.50, A:Y.244, A:R.304 GOL.4: 11 residues within 4Å: Chain A: G.290, R.291, Y.294, P.295, G.296, Y.337 Chain E: Q.267, S.270, E.271, A.274, G.284 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.267, A:R.291 GOL.7: 5 residues within 4Å: Chain B: V.129, G.130, Y.244, Y.248, R.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.244, B:Y.244, B:R.304 GOL.10: 6 residues within 4Å: Chain C: M.62, V.129, G.130, Y.244, Y.248, R.304 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.129, C:Y.244, C:R.304, C:R.304 GOL.14: 6 residues within 4Å: Chain D: I.65, R.235, G.269, V.272, R.278, D.292 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.235, D:R.278, D:R.278, D:T.288 GOL.15: 7 residues within 4Å: Chain A: Q.215 Chain D: S.131, E.133, Q.134, G.153, T.302, D.334 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.131, D:Q.134, D:T.302, A:Q.215 Water bridges: D:S.131

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

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, AZI.13 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:T.167, D:T.167, D:V.168, C:S.372 Water bridges: D:T.167, D:L.169, D:R.193, D:R.193, D:D.260, C:R.373, C:R.373 Salt bridges: D:K.166, C:R.373, C:R.373 pi-Stacking: D:Y.349, D:Y.349

1 x AZI: AZIDE ION(Non-covalent)

AZI.13: 8 residues within 4Å: Chain C: S.344, R.373 Chain D: A.162, G.163, K.166, R.193, Y.315 Ligands: ADP.11 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.163, D:K.166, D:R.193, C:R.373, C:R.373 Water bridges: D:E.192, D:E.192, D:E.192, D:R.193, D:N.261

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

PO4.16: 7 residues within 4Å: Chain E: G.161, A.162, G.163, V.164, G.165, K.166, T.167 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.161, E:G.163, E:V.164, E:G.165, E:K.166, E:T.167, E:T.167, E:T.167

1 x PIT: PICEATANNOL(Non-covalent)

PIT.19: 11 residues within 4Å: Chain B: R.291, E.292 Chain C: E.292, A.293 Chain F: A.282, V.283 Chain G: A.256, T.259, K.260, I.263, E.264 14 PLIP interactions: 7 interactions with chain G, 2 interactions with chain F, 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: G:A.256, G:K.260, G:K.260, G:I.263, F:V.283, B:R.291 Hydrogen bonds: G:T.259, F:V.283, B:E.292 Water bridges: G:S.267, C:A.293, B:R.291, B:R.291 pi-Cation interactions: G:K.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gledhill, J.R. et al., Mechanism of Inhibition of Bovine F1-ATPase by Resveratrol and Related Polyphenols. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2007-08-21

Peptides

ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM: ABC
ATP SYNTHASE SUBUNIT BETA: DEF
ATP SYNTHASE GAMMA CHAIN: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
N

ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM

ATP SYNTHASE SUBUNIT BETA

ATP SYNTHASE GAMMA CHAIN

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