SMTL ID : 3zia.2 (1 other biounit)

The structure of F1-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

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

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, Q.434 Chain D: Y.368 Ligands: MG.2 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.174, A:Q.174, A:T.175, A:G.176, A:K.177, A:T.178, A:A.179, A:Q.432, A:Q.434, A:Q.434, D:S.355, D:Y.368 Water bridges: A:T.178, A:T.178, A:T.178, A:T.178 Salt bridges: A:K.177, A:K.177

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.178, D.271 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.178, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: T.178, D.271 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.178, H2O.3, H2O.3, H2O.3, H2O.5 MG.6: 3 residues within 4Å: Chain C: T.178, D.271 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.178, H2O.6, H2O.6, H2O.6, H2O.8 MG.9: 2 residues within 4Å: Chain D: T.164 Ligands: ADP.8 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.164, H2O.8, H2O.9, H2O.9, H2O.9 MG.12: 4 residues within 4Å: Chain F: T.164, E.189, R.190 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.164, H2O.12, H2O.12, H2O.12, H2O.12

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

ADP.3: 14 residues within 4Å: Chain B: D.172, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, Q.432, Q.434 Chain E: R.356, D.359 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.172, B:Q.174, B:T.175, B:T.175, B:G.176, B:K.177, B:T.178, B:A.179, B:R.364, B:Q.432, B:Q.434, B:Q.434 Water bridges: B:K.177, B:K.177, B:T.178, B:T.178 Salt bridges: B:K.177 ADP.5: 16 residues within 4Å: Chain C: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, Q.434 Chain F: R.356, Y.368 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.174, C:T.175, C:T.175, C:G.176, C:K.177, C:T.178, C:A.179, C:R.364, C:Q.432, C:Q.434, F:R.356 Water bridges: C:T.178, C:E.330 Salt bridges: C:K.177 ADP.8: 13 residues within 4Å: Chain C: R.375 Chain D: G.158, G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, A.421, F.424 Ligands: MG.9 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.158, D:G.160, D:V.161, D:G.162, D:K.163, D:T.164, D:V.165 Water bridges: D:K.163, D:K.163, D:R.190, C:R.375, C:R.375, C:R.375 Salt bridges: D:K.163, C:R.375, C:R.375 pi-Stacking: D:Y.345, D:Y.345 ADP.10: 12 residues within 4Å: Chain E: G.158, G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, A.421, F.424, T.425 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.160, E:V.161, E:G.162, E:K.163, E:T.164, E:T.164, E:T.164, E:V.165, E:Y.345 Water bridges: E:K.163, E:T.164 Salt bridges: E:K.163 pi-Stacking: E:Y.345 ADP.11: 14 residues within 4Å: Chain B: V.373, R.375 Chain F: G.158, G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, A.421, F.424 Ligands: MG.12 20 PLIP interactions: 16 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.160, F:V.161, F:G.162, F:K.163, F:T.164, F:V.165, B:R.375 Water bridges: F:K.163, F:K.163, F:R.190, F:R.190, F:R.190, F:R.190, F:Y.345, B:R.375, B:R.375 Salt bridges: F:K.163, B:R.375 pi-Stacking: F:Y.345, F:Y.345

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 7 residues within 4Å: Chain C: Q.132, Y.246, Y.280, D.299, Y.302, L.303, R.306 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.132, C:D.299, C:R.306, C:R.306 Water bridges: C:Y.280, C:Y.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, G.C. et al., The Structure of F1-ATPase from Saccharomyces Cerevisiae Inhibited by its Regulatory Protein If1. Open Biol. (2013)

Release Date

2013-02-13

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
ATPASE INHIBITOR, MITOCHONDRIAL: J

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

J
J

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

ATPASE INHIBITOR, MITOCHONDRIAL

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