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

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

Coordinates

PDB Format

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: 17 interactions with chain A, 1 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:T.178, A:A.179, A:Q.432, A:Q.434, A:Q.434, D:S.355 Water bridges: A:Q.174, A:K.177, A:K.177, 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: 2 residues within 4Å: Chain B: T.178 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.178, H2O.4, H2O.4, H2O.4, H2O.8 MG.8: 3 residues within 4Å: Chain C: T.178, D.271 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.178, H2O.9, H2O.9, H2O.9, H2O.10 MG.11: 2 residues within 4Å: Chain D: T.164 Ligands: ADP.10 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.164, H2O.10, H2O.11, H2O.11, H2O.11 MG.15: 4 residues within 4Å: Chain F: T.164, E.189, R.190 Ligands: ADP.14 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.164, H2O.15, H2O.15, H2O.15, H2O.15

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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.172, B:Q.174, B:T.175, B:G.176, B:K.177, B:T.178, 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 Salt bridges: B:K.177 ADP.7: 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.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:D.172, C:Q.174, C:T.175, C:G.176, C:K.177, C:T.178, C:T.178, C:A.179, C:R.364, C:Q.432, C:Q.434, F:R.356 Water bridges: C:E.330, C:Q.434 Salt bridges: C:K.177 ADP.10: 14 residues within 4Å: Chain C: R.375 Chain D: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, A.421, F.424 Ligands: MG.11 19 PLIP interactions: 14 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: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.12: 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 9 PLIP interactions: 9 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:V.165 Salt bridges: E:K.163 pi-Stacking: E:Y.345 ADP.14: 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.15 19 PLIP interactions: 15 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:T.164, F:V.165, B:R.375 Water bridges: F:G.158, F:K.163, F:R.190, F:R.190, F:R.190, B:R.375, B:R.375 Salt bridges: F:K.163, B:R.375 pi-Stacking: F:Y.345, F:Y.345

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

EDO.5: 7 residues within 4Å: Chain B: G.292, R.293, G.298 Chain F: S.266, V.279, G.280, Y.281 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.280, B:R.293 Water bridges: F:Y.281, F:Y.281, B:R.293, B:G.298, B:Y.339 EDO.6: 4 residues within 4Å: Chain B: I.363, I.367, T.427, L.430 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.367, B:T.427 EDO.9: 6 residues within 4Å: Chain C: Y.246, Y.280, D.299, Y.302, L.303, R.306 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.246, C:D.299, C:R.306, C:R.306 EDO.13: 3 residues within 4Å: Chain E: A.51, R.231, L.272 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.231 Water bridges: E:R.274 EDO.16: 6 residues within 4Å: Chain F: K.45, L.46, V.47, M.64, D.65, I.99 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.47, F:D.65

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
K

B
L

C
M

D
N

E
O

F
P

G
Q

H
R

I
S

J
T

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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