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A second transient position of ATP on its trail to the nucleotide- binding site of subunit B of the motor protein A1AO ATP synthase
Analyse A second transient position of ATP on its trail to the nucleotide- binding site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EIU
- Type
- protein
- Length
- 844 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase beta chain
- EC
- 3.6.3.14
- UniProt
- Q60187
- Ligands
- ATP, AES
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type ATP synthase beta chain (EC 3.6.3.14) | protein | 418 | 34% helix, 23% strand | Q60187 |
| B | V-type ATP synthase beta chain (EC 3.6.3.14) | protein | 426 | 33% helix, 24% strand | Q60187 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- AES · 4-(2-aminoethyl)benzenesulfonyl fluoride · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.85 | 0.94 | 42 | empty |
| 2 | 958 | 0.76 | 0.79 | 82 | ATP |
| 3 | 370 | 0.68 | 0.81 | 32 | empty |
| 4 | 351 | 0.63 | 0.79 | 53 | empty |
| 5 | 215 | 0.56 | 0.79 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2369 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3EIU · A second transient position of ATP on its trail to the nucleotide-binding site of subunit… · the same entry in another collection · chain A against A, TM-score 1.00
- Q60187 · AlphaFold monomer V2.0 prediction for V-type ATP synthase beta chain (Q60187) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q60187
- Elsewhere: RCSB PDB 3EIU · PDBe 3EIU · UniProt Q60187
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