Research workbench
Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, rotor, rotational state 1
Analyse Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, rotor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDX
- Type
- protein
- Length
- 1,339 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase F1 subunit gamma; F-type H+-transporting ATPase subunit delta; ATP synthase…
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 5 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | ATP synthase F1 subunit gamma | protein | 276 | 59% helix, 12% strand | — |
| H | F-type H+-transporting ATPase subunit delta | protein | 160 | 27% helix, 32% strand | — |
| I | ATP synthase F1 subunit epsilon | protein | 66 | 42% helix, 14% strand | — |
| O, P, Q, R, S, T, U, V, W, X | ATP synthase subunit C | protein | 81 | 77% helix, 9% strand | — |
| 0 | ATPEG1 | protein | 27 | 93% helix, 0% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.79 | 0.81 | 81 | empty |
| 2 | 674 | 0.73 | 0.79 | 53 | empty |
| 3 | 360 | 0.71 | 0.83 | 50 | empty |
| 4 | 207 | 0.58 | 0.80 | 22 | empty |
| 5 | 149 | 0.54 | 0.79 | 19 | empty |
Interfaces
30 interfaces between chains.
- G–H · 2305 Ų buried · 29 hydrogen bonds · protein-protein
- O–P · 1922 Ų buried · 15 hydrogen bonds · protein-protein
- P–Q · 1909 Ų buried · 12 hydrogen bonds · protein-protein
- U–V · 1900 Ų buried · 17 hydrogen bonds · protein-protein
- V–W · 1898 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6TDX · Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, rotor, rotational state… · the same entry in another collection · chain G against G, 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 6TDX · PDBe 6TDX
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