SMTL ID : 8f2k.1

Structure of yeast F1-ATPase determined with 100 micromolar cruentaren A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: R.148, Q.149, T.150, G.151, K.152, T.153, A.154, E.305, F.334, R.339, Q.407, Q.409 Chain F: D.352, Y.361 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:Q.149, A:T.150, A:G.151, A:G.151, A:K.152, A:T.153, A:A.154, A:E.305, A:Q.407, A:Q.409, A:Q.409, F:Y.361 Salt bridges: A:K.152, A:K.152 ATP.3: 13 residues within 4Å: Chain B: R.148, Q.149, T.150, G.151, K.152, T.153, A.154, F.334, R.339, Q.407, Q.409 Chain D: R.349 Ligands: MG.4 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.149, B:G.151, B:G.151, B:K.152, B:T.153, B:A.154, B:R.339, B:Q.407, B:Q.409, B:Q.409 Salt bridges: B:K.152, B:K.152, D:R.349 ATP.5: 14 residues within 4Å: Chain C: R.148, Q.149, T.150, G.151, K.152, T.153, A.154, E.305, F.334, R.339, Q.407, Q.409 Chain E: D.352 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Q.149, C:G.151, C:K.152, C:T.153, C:A.154, C:R.339, C:Q.407, C:Q.409, C:Q.409 Salt bridges: C:K.152, C:K.152 ATP.7: 23 residues within 4Å: Chain B: I.320, S.321, V.348, R.350 Chain E: G.151, A.152, G.153, V.154, G.155, K.156, T.157, V.158, E.182, R.183, E.186, Y.338, P.339, F.411, A.414, F.417, T.418 Ligands: MG.8, XBC.9 17 PLIP interactions: 12 interactions with chain E, 5 interactions with chain B Hydrogen bonds: E:G.153, E:V.154, E:G.155, E:K.156, E:T.157, E:V.158, E:Y.338, B:S.321, B:S.321 Salt bridges: E:K.156, E:K.156, E:R.183, B:R.350, B:R.350, B:R.350 pi-Stacking: E:Y.338, E:Y.338 ATP.10: 21 residues within 4Å: Chain C: I.320, S.321, V.348, R.350 Chain F: G.151, A.152, G.153, V.154, G.155, K.156, T.157, V.158, R.183, Y.338, P.339, F.411, A.414, F.417, T.418 Ligands: MG.11, XBC.12 16 PLIP interactions: 4 interactions with chain C, 12 interactions with chain F Hydrogen bonds: C:I.320, F:G.153, F:V.154, F:G.155, F:K.156, F:T.157, F:T.157, F:V.158 Salt bridges: C:R.350, C:R.350, C:R.350, F:K.156, F:K.156, F:R.183 pi-Stacking: F:Y.338, F:Y.338

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.153, D.246 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.153 MG.4: 3 residues within 4Å: Chain B: T.153, D.246 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.153 MG.6: 3 residues within 4Å: Chain C: T.153, D.246 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.153 MG.8: 4 residues within 4Å: Chain E: T.157, R.183, E.186 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.157 MG.11: 4 residues within 4Å: Chain F: T.157, R.183, E.186 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.157

2 x XBC: Cruentaren A(Non-covalent)

XBC.9: 21 residues within 4Å: Chain B: V.311, Q.326, G.345, L.346, V.348, K.368, L.369, A.372, Q.373, E.376 Chain E: R.330, S.333, E.334, L.335, G.336, Y.338, F.417, T.418, I.420, Y.451 Ligands: ATP.7 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:V.311, B:L.346, B:V.348, B:V.348, B:Q.373, E:F.417, E:T.418 Hydrogen bonds: B:Q.326, E:R.330 XBC.12: 22 residues within 4Å: Chain C: V.311, Q.326, F.328, G.345, L.346, V.348, K.368, L.369, A.372, Q.373, E.376 Chain F: G.153, R.330, S.333, E.334, G.336, Y.338, T.418, I.420, Y.451, M.452 Ligands: ATP.10 14 PLIP interactions: 4 interactions with chain F, 10 interactions with chain C Hydrophobic interactions: F:E.334, C:V.311, C:V.311, C:Q.326, C:F.328, C:L.346, C:V.348, C:V.348, C:L.369, C:Q.373 Hydrogen bonds: F:R.330, F:E.334, C:Q.326 pi-Stacking: F:Y.451

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dou, X. et al., CryoEM Structure with ATP Synthase Enables Late-Stage Diversification of Cruentaren A. Chemistry (2023)

Release Date

2023-04-05

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase subunit gamma: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase subunit gamma

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