MolNFT v1 · #162581 · protein
Cryoem structure of polytomella F-ATP synthase, primary rotary state 2, focussed refinement of F1 head and rotor
6RDE · Mitochondrial ATP synthase subunit C: “Cryoem structure of polytomella F-ATP synthase, primary rotary state 2, focussed refinement of F1 head and…”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.85).…
- PDB
- 6RDE
- Type
- protein
- Length
- 4,502 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial ATP synthase subunit C; Mitochondrial ATP synthase subunit oscp; Epsilon…
- EC
- 7.1.2.2
- UniProt
- D8V7I1, D7P7X6, Q4LDE7, A0ZW40, A0ZW41
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 11 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Mitochondrial ATP synthase subunit C | protein | 74 | 88% helix, 0% strand | — |
| P | Mitochondrial ATP synthase subunit oscp | protein | 113 | 67% helix, 0% strand | D8V7I1 |
| Q | Epsilon: polytomella F-ATP synthase epsilon subunit | protein | 72 | 36% helix, 13% strand | — |
| R | Mitochondrial ATP synthase subunit delta | protein | 177 | 23% helix, 28% strand | D7P7X6 |
| S | ATP synthase gamma chain, mitochondrial | protein | 277 | 57% helix, 14% strand | Q4LDE7 |
| T | ATP synthase subunit alpha | protein | 483 | 39% helix, 20% strand | A0ZW40 |
| U | ATP synthase subunit alpha | protein | 523 | 38% helix, 20% strand | A0ZW40 |
| V | ATP synthase subunit alpha | protein | 520 | 38% helix, 19% strand | A0ZW40 |
| X | ATP synthase subunit beta (EC 7.1.2.2) | protein | 538 | 32% helix, 19% strand | A0ZW41 |
| Y | ATP synthase subunit beta (EC 7.1.2.2) | protein | 520 | 35% helix, 19% strand | A0ZW41 |
| Z | ATP synthase subunit beta (EC 7.1.2.2) | protein | 539 | 33% helix, 18% strand | A0ZW41 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains T, X, U, Z, V, Y
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains T, Y, V, Z
- MG · Magnesium ion · metal · 5 copies · chains T, U, V, Y, Z
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 | 618 | 0.85 | 0.90 | 84 | empty |
| 2 | 656 | 0.85 | 0.89 | 82 | ATP, MG |
| 3 | 500 | 0.84 | 0.91 | 66 | empty |
| 4 | 631 | 0.84 | 0.89 | 62 | ATP, MG |
| 5 | 1157 | 0.83 | 0.84 | 119 | ADP, MG |
Interfaces
50 interfaces between chains.
- V–Z · 4053 Ų buried · 40 hydrogen bonds · protein-protein
- U–X · 3638 Ų buried · 36 hydrogen bonds · protein-protein
- T–Y · 3345 Ų buried · 33 hydrogen bonds · protein-protein
- U–Z · 2623 Ų buried · 25 hydrogen bonds · protein-protein
- V–Y · 2592 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6RDE · CryoEM structure of Polytomella F-ATP synthase, Primary rotary state 2, focussed… · 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
- Every structure of UniProt D8V7I1
- Every structure of UniProt D7P7X6
- Every structure of UniProt Q4LDE7
- Every structure of UniProt A0ZW40
- Every structure of UniProt A0ZW41
- Elsewhere: RCSB PDB 6RDE · PDBe 6RDE · UniProt D8V7I1 · UniProt D7P7X6 · UniProt Q4LDE7 · UniProt A0ZW40 · UniProt A0ZW41
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