MolNFT v1 · #162572 · protein
Cryoem structure of polytomella F-ATP synthase, focussed refinement of fo and peripheral stalk, C2 symmetry
6RD5 · Asa-10: polytomella F-ATP synthase associated subunit 10: “Cryoem structure of polytomella F-ATP synthase, focussed refinement of fo and peripheral stalk, C2 symmetry”. Electron microscopy, 2 ligands (PEV, ZN), 16 pockets (best…
- PDB
- 6RD5
- Type
- protein
- Length
- 1,566 residues
- Chains
- 8
- 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, H8PGG3
- Ligands
- PEV, ZN
- Pockets
- 16 · best druggability 0.88
Structure
electron microscopy · 8 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | Asa-10: polytomella F-ATP synthase associated subunit 10 | protein | 79 | 34% helix, 3% strand | — |
| 1 | ATP synthase associated protein ASA1 | protein | 595 | 62% helix, 1% strand | Q85JD5 |
| 3 | Mitochondrial F1F0 ATP synthase associated 32 kda protein | protein | 244 | 69% helix, 2% strand | K0J903 |
| 5 | Mitochondrial F1F0 ATP synthase associated 14 kda protein | protein | 123 | 67% helix, 0% strand | A0A024FSR7 |
| 6 | Mitochondrial ATP synthase subunit ASA6 | protein | 124 | 62% helix, 0% strand | D7P897 |
| 8 | Mitochondrial ATP synthase subunit ASA8 | protein | 88 | 58% helix, 0% strand | D8V7I7 |
| 9 | Mitochondrial ATP synthase subunit ASA9 | protein | 96 | 60% helix, 0% strand | — |
| M | Mitochondrial ATP synthase subunit 6 | protein | 217 | 68% helix, 2% strand | H8PGG3 |
Ligands and binding sites
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 11 copies · chains 0, 5, 6, 8, M, 1, 9
- ZN · Zinc ion · metal · chains 6, M
- LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains 6, M, 8, 0, 9
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.88 | 0.89 | 97 | empty |
| 2 | 591 | 0.70 | 0.78 | 66 | PEV, ZN |
| 3 | 180 | 0.65 | 0.85 | 25 | empty |
| 4 | 258 | 0.62 | 0.81 | 59 | empty |
| 5 | 434 | 0.60 | 0.76 | 56 | empty |
Interfaces
24 interfaces between chains.
- 1–5 · 3933 Ų buried · 32 hydrogen bonds · protein-protein
- 1–6 · 2284 Ų buried · 19 hydrogen bonds · protein-protein
- 1–8 · 1366 Ų buried · 11 hydrogen bonds · protein-protein
- 6–M · 1231 Ų buried · 9 hydrogen bonds · protein-protein
- 1–3 · 1141 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6RD5 · CryoEM structure of Polytomella F-ATP synthase, focussed refinement of Fo and peripheral… · the same entry in another collection · chain 0 against 0, 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 H8PGG3
- Elsewhere: RCSB PDB 6RD5 · PDBe 6RD5 · UniProt Q85JD5 · UniProt K0J903 · UniProt A0A024FSR7 · UniProt D7P897 · UniProt D8V7I7 · UniProt H8PGG3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.