MolNFT v1 · #33938 · protein
Subunit F of V-type ATPASE/SYNTHASE
2D00 · V-type ATP synthase subunit F: “Subunit F of V-type ATPASE/SYNTHASE”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.76). MolNFT v1 #33938 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D00
- Type
- protein
- Length
- 654 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase subunit F
- EC
- 3.6.3.14
- UniProt
- P74903
- Ligands
- CA
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | V-type ATP synthase subunit F (EC 3.6.3.14) | protein | 109 | 45% helix, 17% strand | P74903 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, E, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.76 | 0.79 | 100 | empty |
| 2 | 502 | 0.69 | 0.79 | 52 | CA |
| 3 | 402 | 0.65 | 0.79 | 45 | empty |
| 4 | 80 | 0.55 | 0.86 | 14 | empty |
| 5 | 67 | 0.40 | 0.80 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–F · 2418 Ų buried · 27 hydrogen bonds · protein-protein
- C–E · 2374 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 2320 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1055 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 886 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 P74903
- Elsewhere: RCSB PDB 2D00 · PDBe 2D00 · UniProt P74903
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