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Cryoem structure of polytomella F-ATP synthase, C-ring position 1, focussed refinement of fo and peripheral stalk
Analyse Cryoem structure of polytomella F-ATP synthase, C-ring position 1, focussed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RD7
- Type
- protein
- Length
- 2,309 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asa-10: polytomella F-ATP synthase associated subunit 10; ATP synthase associated protein…
- UniProt
- Q85JD5, K0J903, A0A024FSR7, D7P897, D8V7I7, D7P7X5, H8PGG3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 9 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Asa-10: polytomella F-ATP synthase associated subunit 10 | protein | 81 | 40% helix, 2% strand | — |
| 1 | ATP synthase associated protein ASA1 | protein | 595 | 64% helix, 1% strand | Q85JD5 |
| 3 | Mitochondrial F1F0 ATP synthase associated 32 kda protein | protein | 245 | 66% helix, 2% strand | K0J903 |
| 5 | Mitochondrial F1F0 ATP synthase associated 14 kda protein | protein | 123 | 70% helix, 0% strand | A0A024FSR7 |
| 6 | Mitochondrial ATP synthase subunit ASA6 | protein | 124 | 64% helix, 0% strand | D7P897 |
| 8 | Mitochondrial ATP synthase subunit ASA8 | protein | 88 | 63% helix, 0% strand | D8V7I7 |
| 9 | Asa-9: polytomella F-ATP synthase associated subunit 9 | protein | 96 | 54% helix, 0% strand | — |
| A, B, C, D, E, F, G, H, I, J | Mitochondrial ATP synthase subunit C | protein | 74 | 95% helix, 0% strand | D7P7X5 |
| M | Mitochondrial ATP synthase subunit 6 | protein | 217 | 69% helix, 2% strand | H8PGG3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 6, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.88 | 0.89 | 95 | empty |
| 2 | 781 | 0.75 | 0.79 | 59 | empty |
| 3 | 1062 | 0.70 | 0.74 | 88 | empty |
| 4 | 601 | 0.68 | 0.77 | 73 | empty |
| 5 | 274 | 0.65 | 0.82 | 51 | empty |
Interfaces
42 interfaces between chains.
- 1–5 · 3970 Ų buried · 35 hydrogen bonds · protein-protein
- 1–6 · 2299 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1549 Ų buried · 7 hydrogen bonds · protein-protein
- A–J · 1536 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 1533 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6RD7 · CryoEM structure of Polytomella F-ATP synthase, c-ring position 1, focussed refinement of… · the same entry in another collection · chain 1 against 1, 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
- Every structure of UniProt Q85JD5
- Every structure of UniProt K0J903
- Every structure of UniProt A0A024FSR7
- Every structure of UniProt D7P897
- Every structure of UniProt D8V7I7
- Every structure of UniProt D7P7X5
- Every structure of UniProt H8PGG3
- Elsewhere: RCSB PDB 6RD7 · PDBe 6RD7 · UniProt Q85JD5 · UniProt K0J903 · UniProt A0A024FSR7 · UniProt D7P897 · UniProt D8V7I7 · UniProt D7P7X5 · UniProt H8PGG3
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