Research workbench
Crystal structure of subunit F of V-ATPase from S. cerevisiae
Analyse Crystal structure of subunit F of V-ATPase from S. cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IX9
- Type
- protein
- Length
- 367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit F
- EC
- 3.6.3.14
- UniProt
- P39111
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | V-type proton ATPase subunit F (EC 3.6.3.14) | protein | 92 | 36% helix, 24% strand | P39111 |
| B | V-type proton ATPase subunit F (EC 3.6.3.14) | protein | 93 | 38% helix, 20% strand | P39111 |
| D | V-type proton ATPase subunit F (EC 3.6.3.14) | protein | 90 | 38% helix, 22% strand | P39111 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.64 | 0.75 | 54 | GOL |
| 2 | 69 | 0.36 | 0.77 | 14 | GOL |
| 3 | 111 | 0.35 | 0.74 | 21 | empty |
| 4 | 58 | 0.30 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 515 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 145 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 74 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4IX9 · Crystal structure of subunit F of V-ATPase from S. cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- P39111 · AlphaFold monomer V2.0 prediction for V-type proton ATPase subunit F (P39111) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P39111
- Elsewhere: RCSB PDB 4IX9 · PDBe 4IX9 · UniProt P39111
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