SMTL ID : 2jdi.1

Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

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

Ligands

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

ANP.1: 16 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, P.363, Q.430, G.431, Q.432 Chain D: Y.372 Ligands: MG.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.172, A:Q.172, A:T.173, A:T.173, A:G.174, A:K.175, A:K.175, A:T.176, A:S.177, A:S.177, A:Q.430, A:Q.432, D:S.359 Water bridges: A:T.176, A:T.176, A:S.177, A:E.328, A:Q.432, A:Q.432, A:Y.433, A:Y.433 ANP.3: 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, P.363, Q.430, Q.432 Chain E: R.360, D.363 Ligands: MG.4 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.172, B:Q.172, B:T.173, B:G.174, B:K.175, B:K.175, B:T.176, B:S.177, B:S.177, B:R.362, B:Q.430, B:Q.432, E:R.360, E:R.360, E:D.363 Water bridges: B:T.176, B:Y.433 ANP.5: 15 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, Q.432 Chain F: Y.372 Ligands: MG.6 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:K.175, C:T.176, C:S.177, C:S.177, C:R.362, C:Q.430, C:Q.432 Water bridges: C:Q.172, C:T.176, C:T.176, C:S.177, C:Q.432, C:Q.432, F:S.359, F:S.359 ANP.7: 22 residues within 4Å: Chain C: I.343, S.344, V.371, S.372, R.373 Chain D: 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.8 26 PLIP interactions: 20 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:G.163, D:V.164, D:G.165, D:K.166, D:K.166, D:K.166, D:K.166, D:T.167, D:V.168, D:R.193, D:R.193, C:S.372, C:R.373, C:R.373 Water bridges: D:K.166, D:L.169, D:E.192, D:E.192, D:N.261, D:R.264, D:Q.420, C:S.372, C:R.373 pi-Stacking: D:Y.349, D:Y.349 Salt bridges: C:R.373 ANP.9: 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.10 21 PLIP interactions: 5 interactions with chain B, 16 interactions with chain F Hydrogen bonds: B:R.373, B:R.373, F:G.163, F:V.164, F:G.165, F:K.166, F:K.166, F:T.167, F:V.168, F:R.193, F:R.193 Water bridges: B:S.344, B:S.344, F:K.166, F:T.167, F:E.192, F:D.260, F:Q.420 Salt bridges: 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: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.176, H2O.6, H2O.8, H2O.14 MG.4: 3 residues within 4Å: Chain B: T.176, D.269 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.176, H2O.21, H2O.23, H2O.27 MG.6: 3 residues within 4Å: Chain C: T.176, D.269 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.176, H2O.33, H2O.35, H2O.41 MG.8: 4 residues within 4Å: Chain D: T.167, R.193, D.260 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.167, H2O.48, H2O.50, H2O.56 MG.10: 4 residues within 4Å: Chain F: T.167, R.193, D.260 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.167, H2O.75, H2O.77, H2O.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowler, M.W. et al., Ground State Structure of F1-ATPase from Bovine Heart Mitochondria at 1.9 A Resolution. J.Biol.Chem. (2007)

Release Date

2007-03-13

Peptides

ATP SYNTHASE SUBUNIT ALPHA HEART ISOFORM: ABC
ATP SYNTHASE SUBUNIT BETA: 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 SUBUNIT ALPHA HEART ISOFORM

ATP SYNTHASE SUBUNIT BETA

ATP SYNTHASE GAMMA CHAIN

ATP SYNTHASE DELTA CHAIN

ATP SYNTHASE EPSILON CHAIN

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