Research workbench
Structural characterization for the nucleotide binding ability of subunit a of the A1AO ATP synthase
Analyse Structural characterization for the nucleotide binding ability of subunit a of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ND9
- Type
- protein
- Length
- 508 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase alpha chain
- EC
- 3.6.3.14
- UniProt
- O57728
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 508 | 36% helix, 20% strand | O57728 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.97 | 20 | empty |
| 2 | 135 | 0.55 | 0.81 | 25 | empty |
| 3 | 111 | 0.50 | 0.81 | 17 | empty |
| 4 | 161 | 0.46 | 0.76 | 24 | empty |
| 5 | 71 | 0.44 | 0.81 | 16 | empty |
Compared structures
- 3ND9 · Structural characterization for the nucleotide binding ability of subunit A of the A1AO… · the same entry in another collection · chain A against A, TM-score 1.00
- O57728 · AlphaFold monomer V2.0 prediction for V-type ATP synthase alpha chain (O57728) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O57728
- Elsewhere: RCSB PDB 3ND9 · PDBe 3ND9 · UniProt O57728
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