SMTL ID : 2ck3.1

Azide inhibited bovine F1-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

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

Ligands

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

ANP.1: 15 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, Q.432 Chain D: Y.372 Ligands: MG.2 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.172, 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:E.328, A:E.328, A:Q.430, A:Q.432, D:Y.372 Water bridges: A:Q.172, A:T.176, A:S.177, A:D.270, A:Q.432, A:Y.433, A:Y.433, D:S.359 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, G.431, Q.432 Chain E: R.360 Ligands: MG.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:Q.172, B:Q.172, B:T.173, B:T.173, B:G.174, B:K.175, B:K.175, B:T.176, B:S.177, B:S.177, B:Q.430, B:Q.432 Water bridges: B:Q.172, B:K.175, B:D.270, B:D.270, E:R.360, E:R.360 ANP.5: 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.6 21 PLIP interactions: 19 interactions with chain C, 2 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, C:Y.433, C:Y.433, F:Y.372 Water bridges: C:Q.172, C:T.176, C:T.176, C:T.176, C:E.328, F:S.359 ANP.11: 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.12 24 PLIP interactions: 19 interactions with chain F, 5 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:T.167, F:V.168, F:R.193, F:R.193, B:R.373, B:R.373 Water bridges: F:K.166, F:T.167, F:L.169, F:E.192, F:E.196, F:D.260, F:Q.420, B:S.344, 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: 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.7, H2O.9, H2O.15 MG.4: 2 residues within 4Å: Chain B: T.176 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.176, H2O.23, H2O.26, H2O.31 MG.6: 2 residues within 4Å: Chain C: T.176 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.176, H2O.37, H2O.39, H2O.45 MG.8: 3 residues within 4Å: Chain D: T.167, R.193 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.167, H2O.52, H2O.53, H2O.60, H2O.60 MG.12: 3 residues within 4Å: Chain F: T.167, R.193 Ligands: ANP.11 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.167, H2O.79, H2O.81, H2O.88

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

ADP.7: 16 residues within 4Å: Chain C: 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.8, AZI.9 21 PLIP interactions: 6 interactions with chain C, 15 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 Water bridges: C:S.372, C:R.373, C:R.373, D:T.167, D:T.167, D:L.169, D:R.193, D:R.193, D:Q.420 Salt bridges: C:R.373, C:R.373, D:K.166 pi-Stacking: D:Y.349, D:Y.349

1 x AZI: AZIDE ION(Non-covalent)

AZI.9: 9 residues within 4Å: Chain C: I.343, S.344, R.373 Chain D: A.162, G.163, K.166, R.193, Y.315 Ligands: ADP.7 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:S.344, C:R.373, C:R.373, D:G.163, D:K.166, D:R.193 Water bridges: D:E.192, D:R.193, D:R.193, D:R.193, D:R.264, D:R.264

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

PO4.10: 6 residues within 4Å: Chain E: A.162, G.163, V.164, G.165, K.166, T.167 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.163, E:V.164, E:G.165, E:K.166, E:T.167 Water bridges: E:G.161, E:T.167, E:V.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowler, M.W. et al., How Azide Inhibits ATP Hydrolysis by the F-Atpases. Proc.Natl.Acad.Sci.USA (2006)

Release Date

2006-05-08

Peptides

ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL: ABC
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL: DEF
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL: G
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL: H
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL: 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, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL

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