Research workbench
Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, peripheral stalk, rotational state 1
Analyse Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, peripheral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDW
- Type
- protein
- Length
- 841 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPTB1; Subunit D; ATPTB3; ATPTB4; Oligomycin sensitivity conferrring protein (oscp)…
- Pockets
- 15 · best druggability 0.70
Structure
electron microscopy · 7 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPTB1 | protein | 25 | 48% helix, 0% strand | — |
| H | Subunit D | protein | 249 | 68% helix, 0% strand | — |
| B | ATPTB3 | protein | 327 | 50% helix, 15% strand | — |
| C | ATPTB4 | protein | 157 | 73% helix, 0% strand | — |
| M | Oligomycin sensitivity conferrring protein (oscp) | protein | 43 | 44% helix, 0% strand | — |
| N | Subunit B | protein | 31 | 87% helix, 0% strand | — |
| T | Subunit 8 | protein | 9 | 0% helix, 0% strand | — |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.70 | 0.79 | 62 | empty |
| 2 | 615 | 0.67 | 0.77 | 55 | empty |
| 3 | 273 | 0.67 | 0.83 | 35 | empty |
| 4 | 115 | 0.64 | 0.88 | 23 | empty |
| 5 | 143 | 0.59 | 0.84 | 26 | empty |
Interfaces
11 interfaces between chains.
- H–C · 1609 Ų buried · 14 hydrogen bonds · protein-protein
- H–N · 1380 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 1204 Ų buried · 14 hydrogen bonds · protein-protein
- H–B · 1005 Ų buried · 5 hydrogen bonds · protein-protein
- H–M · 922 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6TDW · Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, peripheral stalk… · the same entry in another collection · chain A against A, 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 6TDW · PDBe 6TDW
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