SMTL ID : 5ik2.2 (1 other biounit)

Caldalaklibacillus thermarum F1-ATPase (epsilon mutant)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-3-1-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: D.147, R.148, Q.149, T.150, G.151, K.152, T.153, T.154, F.326, R.331, P.332, Q.399, E.401 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:D.147, A:Q.149, A:T.150, A:T.150, A:G.151, A:K.152, A:T.153, A:T.154, A:T.154, A:R.331, A:Q.399 Water bridges: A:E.297, D:Y.357 Salt bridges: A:K.152 ADP.4: 13 residues within 4Å: Chain B: D.147, Q.149, T.150, G.151, K.152, T.153, T.154, F.326, R.331, Q.399, D.400, E.401 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.147, B:Q.149, B:T.150, B:G.151, B:K.152, B:T.153, B:T.154, B:T.154, B:R.331, B:Q.399, B:E.401 Water bridges: B:R.331 Salt bridges: B:K.152 pi-Stacking: B:F.326 ADP.7: 16 residues within 4Å: Chain C: D.147, R.148, Q.149, T.150, G.151, K.152, T.153, T.154, F.326, R.331, P.332, Q.399, D.400, E.401 Chain F: Y.357 Ligands: MG.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:D.147, C:Q.149, C:T.150, C:G.151, C:K.152, C:T.153, C:T.154, C:T.154, C:Q.399, C:E.401, F:Y.357 Water bridges: C:Q.149, C:Q.149 Salt bridges: C:K.152 pi-Stacking: C:F.326 ADP.10: 16 residues within 4Å: Chain C: V.340, S.341, R.342 Chain D: G.152, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407, A.410, F.413, T.414 Ligands: MG.11 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.152, D:G.154, D:V.155, D:G.156, D:K.157, D:T.158, D:V.159, D:Y.334, C:S.341 Water bridges: D:K.157, D:K.157, D:R.184, D:Q.405, C:R.342 Salt bridges: D:K.157, C:R.342, C:R.342 pi-Stacking: D:Y.334, D:Y.334 ADP.12: 12 residues within 4Å: Chain E: G.152, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407, A.410, F.413, T.414 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.152, E:G.154, E:V.155, E:G.156, E:K.157, E:T.158, E:T.158, E:V.159, E:Y.334 Water bridges: E:Q.405 pi-Stacking: E:Y.334, E:Y.334 ADP.18: 13 residues within 4Å: Chain B: R.342 Chain F: G.152, G.154, V.155, G.156, K.157, T.158, V.159, Y.334, F.407, A.410, T.414 Ligands: MG.19 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.152, F:G.154, F:V.155, F:G.156, F:K.157, F:T.158, F:V.159 Water bridges: F:K.157 Salt bridges: F:K.157 pi-Stacking: F:Y.334, F:Y.334

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.153 Ligands: ADP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.153, H2O.2 MG.5: 3 residues within 4Å: Chain B: T.153, D.238 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.153 MG.8: 3 residues within 4Å: Chain C: T.153, D.238 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.153 MG.11: 3 residues within 4Å: Chain D: T.158, R.184 Ligands: ADP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.158 MG.19: 4 residues within 4Å: Chain F: T.158, E.183, R.184 Ligands: ADP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.158

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: G.259, R.260, Y.263, P.264, G.265, Y.306 Chain E: S.255, E.256, A.259 Ligands: GOL.17 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.255, A:R.260, A:Y.263 GOL.6: 5 residues within 4Å: Chain B: V.330, P.332, V.334, V.336, R.367 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.334, B:R.367 GOL.9: 6 residues within 4Å: Chain C: M.133, V.330, V.334, V.336, R.367, V.394 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.334, C:R.367 Water bridges: C:V.336 GOL.14: 3 residues within 4Å: Chain E: N.91, I.97, E.213 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.91, E:E.213 Water bridges: E:V.92 GOL.15: 7 residues within 4Å: Chain E: Y.27, H.112, R.113, L.223, Q.280, R.284 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:H.112, E:R.113, E:Q.280, E:R.284 GOL.16: 6 residues within 4Å: Chain B: P.55, Y.56, T.57 Chain E: Y.27, Q.280 Ligands: GOL.15 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Y.56, B:Y.56, B:T.57, E:Q.280 GOL.17: 7 residues within 4Å: Chain A: R.260, Y.306 Chain E: S.255, V.268, G.269, Y.270 Ligands: GOL.3 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.255, A:R.260 GOL.20: 6 residues within 4Å: Chain C: L.92, Q.179, E.207 Chain F: P.116, E.117, F.118 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:E.117, F:F.118, C:Q.179 Water bridges: F:P.116, F:E.283, C:S.204, C:S.204 GOL.21: 6 residues within 4Å: Chain B: G.259, Y.263, G.265 Chain F: S.255, V.268, Y.270 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:S.255, F:S.255, F:V.268, B:R.260 Water bridges: F:Y.270, F:Y.270, F:D.308, B:G.265

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

PO4.13: 6 residues within 4Å: Chain A: R.342 Chain E: K.157, R.184, D.245, N.246, R.249 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.246 Water bridges: E:R.249 Salt bridges: E:K.157, E:R.184, E:R.249, A:R.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferguson, S.A. et al., Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-09-21

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

E
M

F
N

G
O

H
P

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

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