Research workbench
Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, OSCP/F1/C-ring, rotational state 3
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
- 6TE0
- Type
- protein
- Length
- 5,136 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; Ribonucleoprotein P18; Oligomycin…
- Ligands
- ATP, ADP, TRT, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 10 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | ATP synthase subunit alpha | protein | 528 | 40% helix, 17% strand | — |
| A | ATP synthase subunit alpha | protein | 526 | 40% helix, 14% strand | — |
| B | ATP synthase subunit alpha | protein | 529 | 40% helix, 16% strand | — |
| F, D, E | ATP synthase subunit beta | protein | 487 | 34% helix, 18% strand | — |
| L, J, K | Ribonucleoprotein P18 | protein | 170 | 54% helix, 1% strand | — |
| M | Oligomycin sensitivity conferring protein (oscp) | protein | 243 | 51% helix, 10% strand | — |
| G | ATP synthase F1 subunit gamma protein | protein | 303 | 59% helix, 12% strand | — |
| H | ATP synthase subunit delta | protein | 160 | 28% helix, 34% strand | — |
| I | ATP synthase subunit epsilon | protein | 66 | 36% helix, 12% strand | — |
| O, P, Q, R, S, T, U, V, W, X | ATP synthase subunit C | protein | 81 | 74% helix, 9% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains C, F, A, D, B, E
- ADP · Adenosine-5'-diphosphate · ligand · chains B, F
- TRT · Fragment of triton X-100 · ligand · chains A, D
- MG · Magnesium ion · metal · 5 copies · chains C, A, B, F, E
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 | 847 | 0.88 | 0.91 | 108 | empty |
| 2 | 849 | 0.85 | 0.87 | 87 | ATP, MG |
| 3 | 941 | 0.84 | 0.85 | 81 | ATP, MG |
| 4 | 378 | 0.84 | 0.93 | 47 | empty |
| 5 | 858 | 0.83 | 0.85 | 93 | ADP |
Interfaces
54 interfaces between chains.
- A–J · 2894 Ų buried · 22 hydrogen bonds · protein-protein
- C–L · 2851 Ų buried · 24 hydrogen bonds · protein-protein
- B–K · 2848 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 2736 Ų buried · 40 hydrogen bonds · protein-protein
- C–F · 2725 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6TE0 · Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring… · the same entry in another collection · chain C against C, 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 6TE0 · PDBe 6TE0
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