SMTL ID : 1e79.1

Bovine F1-ATPase inhibited by DCCD (dicyclohexylcarbodiimide)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-3-3-1-1-1-mer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.328, F.357, R.362, P.363, Q.430, Q.432 Chain D: Y.372 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Q.172, A:T.173, A:T.173, A:G.174, A:K.175, A:T.176, A:S.177, A:S.177, A:Q.430 Water bridges: A:Q.172, A:K.175, A:K.175, A:K.175, A:T.176, A:T.176, A:Q.432, A:Y.433 Salt bridges: A:K.175, A:K.175 ATP.6: 15 residues within 4Å: Chain C: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, E.328, F.357, R.362, Q.430, Q.432 Chain F: Y.372 Ligands: MG.7 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:S.177, C:E.328, C:Q.430, C:Q.432 Water bridges: C:Q.172, C:K.175, C:K.175, C:T.176, C:T.176, F:S.359, F:M.362 Salt bridges: C:K.175, C:K.175

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.176, D.269 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.176, H2O.3, H2O.7 MG.4: 2 residues within 4Å: Chain B: T.176 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.176, H2O.9, H2O.9, H2O.12, H2O.12 MG.7: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.6 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.176, H2O.15, H2O.18 MG.9: 5 residues within 4Å: Chain D: T.167, R.193, E.196, D.260 Ligands: ADP.8 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.167, H2O.21, H2O.24, H2O.24 MG.13: 3 residues within 4Å: Chain F: T.167, R.193 Ligands: ADP.12 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.167, H2O.30, H2O.30, H2O.31, H2O.34

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

ADP.3: 13 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.357, R.362, Q.430, Q.432 Chain E: R.360 Ligands: MG.4 20 PLIP interactions: 19 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:R.362, B:Q.430, B:Q.432, E:R.360 Water bridges: B:K.175, B:K.175, B:K.175, B:K.175, B:K.175, B:K.175, B:T.176, B:T.176 Salt bridges: B:K.175 ADP.8: 15 residues within 4Å: Chain C: S.372, R.373 Chain D: 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.9 23 PLIP interactions: 16 interactions with chain D, 7 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, D:Y.349, C:S.372 Water bridges: D:K.166, D:K.166, D:T.167, D:R.193, D:Q.420, C:R.373, C:R.373, 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 ADP.12: 12 residues within 4Å: Chain B: R.373 Chain F: G.161, G.163, V.164, G.165, K.166, T.167, V.168, Y.349, F.422, F.428 Ligands: MG.13 21 PLIP interactions: 19 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, F:Y.349, B:R.373, B:R.373 Water bridges: F:G.161, F:K.166, F:T.167, F:T.167, F:R.193, F:R.193, F:R.193, F:D.260, F:Y.349 Salt bridges: F:K.166 pi-Stacking: F:Y.349, F:Y.349

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: V.129, G.130, Y.244, Y.248, R.304 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.244, B:R.304, B:R.304 Water bridges: B:V.129, B:R.304

1 x DCW: DICYCLOHEXYLUREA(Covalent)

DCW.10: 5 residues within 4Å: Chain D: V.168, M.171, E.203, V.424, F.428 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.168, D:E.203, D:V.424, D:V.424, D:F.428

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 3 residues within 4Å: Chain A: R.373 Chain E: R.193, R.264 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain A Water bridges: E:R.264, E:R.264 Salt bridges: E:R.193, E:R.264, A:R.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibbons, C. et al., The Structure of the Central Stalk in Bovine F(1)-ATPase at 2.4 A Resolution. Nat.Struct.Biol. (2000)

Release Date

2000-11-03

Peptides

ATP SYNTHASE ALPHA CHAIN HEART ISOFORM: ABC
ATP SYNTHASE BETA CHAIN: DEF
ATP SYNTHASE GAMMA CHAIN: G
ATP SYNTHASE DELTA CHAIN: H
ATP SYNTHASE EPSILON CHAIN: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

ATP SYNTHASE ALPHA CHAIN HEART ISOFORM

ATP SYNTHASE BETA CHAIN

ATP SYNTHASE GAMMA CHAIN

ATP SYNTHASE DELTA CHAIN

ATP SYNTHASE EPSILON CHAIN

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