MolNFT v1 · #115230 · protein
Structure at 2.3 a of the ALPHA/BETA monomer of the F-ATPase from paracoccus denitrificans
5CDF · ATP synthase subunit alpha: “Structure at 2.3 a of the ALPHA/BETA monomer of the F-ATPase from paracoccus denitrificans”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.74). MolNFT v1 #115230 on GenesisL1: 3D…
- PDB
- 5CDF
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta
- EC
- 3.6.3.14
- UniProt
- A1B8N8, A1B8P0
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 488 | 41% helix, 20% strand | A1B8N8 |
| E | ATP synthase subunit beta (EC 3.6.3.14) | protein | 456 | 36% helix, 21% strand | A1B8P0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.74 | 0.83 | 76 | GOL |
| 2 | 699 | 0.71 | 0.78 | 73 | GOL |
| 3 | 210 | 0.63 | 0.83 | 29 | empty |
| 4 | 98 | 0.59 | 0.86 | 21 | empty |
| 5 | 82 | 0.50 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–E · 2097 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5CDF · Structure at 2.3 A of the alpha/beta monomer of the F-ATPase from Paracoccus denitrificans · the same entry in another collection · chain A against A, TM-score 1.00
- A1B8N8 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha (A1B8N8) · a predicted model of the same protein · chain A against A, TM-score 0.99
- A1B8P0 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta (A1B8P0) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 A1B8N8
- Every structure of UniProt A1B8P0
- Elsewhere: RCSB PDB 5CDF · PDBe 5CDF · UniProt A1B8N8 · UniProt A1B8P0
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