MolNFT v1 · #167323 · protein
Fphf, staphylococcus aureus fluorophosphonate-binding serine hydrolases F, apo form
6VH9 · Esterase family protein: “Fphf, staphylococcus aureus fluorophosphonate-binding serine hydrolases F, apo form”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.87). MolNFT v1 #167323 on GenesisL1: 3D structure…
- PDB
- 6VH9
- Type
- protein
- Length
- 1,020 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase family protein
- EC
- 3.1.2.12
- UniProt
- A0A0D6GS23
- Ligands
- NA
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Esterase family protein (EC 3.1.2.12) | protein | 255 | 36% helix, 23% strand | A0A0D6GS23 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.87 | 0.95 | 44 | empty |
| 2 | 77 | 0.75 | 0.98 | 28 | empty |
| 3 | 75 | 0.74 | 0.98 | 26 | empty |
| 4 | 244 | 0.56 | 0.77 | 28 | NA |
| 5 | 235 | 0.54 | 0.77 | 28 | NA |
Interfaces
6 interfaces between chains.
- A–B · 1207 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1185 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1131 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 619 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6VH9 · FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, apo form · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0D6GS23
- Elsewhere: RCSB PDB 6VH9 · PDBe 6VH9 · UniProt A0A0D6GS23
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