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Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, OSCP/F1/C-ring in rotational state 1
Analyse Cryo-EM structure of euglena gracilis mitochondrial ATP synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDY
- Type
- protein
- Length
- 5,289 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase subunit gamma; ATP…
- Ligands
- ATP, ADP, TRT, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 12 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP synthase subunit alpha | protein | 526 | 40% helix, 17% strand | — |
| C | ATP synthase subunit alpha | protein | 529 | 40% helix, 18% strand | — |
| D, E, F | ATP synthase subunit beta | protein | 487 | 35% helix, 19% strand | — |
| G | ATP synthase subunit gamma | protein | 303 | 60% helix, 12% strand | — |
| H | ATP synthase subunit delta | protein | 160 | 28% helix, 34% strand | — |
| I | ATP synthase subunit epsilon | protein | 66 | 32% helix, 12% strand | — |
| J, K, L | P18 | protein | 170 | 54% helix, 2% strand | — |
| M | Oligomycin sensitivity conferring protein (oscp) | protein | 243 | 53% helix, 11% strand | — |
| N | Inhibitor of F1 (IF1) | protein | 49 | 47% helix, 4% strand | — |
| O, P, Q, R, S, T, U, V, W, X | ATP synthase subunit C | protein | 81 | 75% helix, 9% strand | — |
| h | ATP synthase subunit D | protein | 49 | 84% helix, 0% strand | — |
| c | ATPTB4 | protein | 57 | 70% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · chains C, D
- TRT · Fragment of triton X-100 · ligand · chains B, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.87 | 0.91 | 93 | empty |
| 2 | 823 | 0.87 | 0.89 | 92 | ADP, MG |
| 3 | 1198 | 0.84 | 0.85 | 95 | ATP, MG |
| 4 | 982 | 0.84 | 0.85 | 93 | ATP, MG |
| 5 | 438 | 0.84 | 0.91 | 51 | empty |
Interfaces
62 interfaces between chains.
- C–L · 2854 Ų buried · 28 hydrogen bonds · protein-protein
- A–J · 2851 Ų buried · 24 hydrogen bonds · protein-protein
- B–K · 2834 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2674 Ų buried · 35 hydrogen bonds · protein-protein
- C–F · 2571 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6TDY · Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring in… · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6TDY · PDBe 6TDY
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