MolNFT v1 · #167327 · protein
Fphf, staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT129 bound
6VHD · Esterase family protein: “Fphf, staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT129 bound”. X-ray diffraction, 1 ligand (6WG), 9 pockets (best druggability 0.87). MolNFT v1 #167327 on GenesisL1: 3D structure…
- PDB
- 6VHD
- 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
- 6WG
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Esterase family protein (EC 3.1.2.12) | protein | 255 | 38% helix, 21% strand | A0A0D6GS23 |
Ligands and binding sites
- 6WG · (2~{R})-2-phenylpiperidine-1-carbaldehyde · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.87 | 0.95 | 46 | empty |
| 2 | 75 | 0.74 | 0.98 | 27 | empty |
| 3 | 69 | 0.73 | 0.98 | 26 | empty |
| 4 | 264 | 0.55 | 0.76 | 28 | 6WG |
| 5 | 256 | 0.55 | 0.77 | 28 | 6WG |
Interfaces
6 interfaces between chains.
- A–B · 1210 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1200 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1187 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1150 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 604 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6VHD · FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT129 bound · 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 6VHD · PDBe 6VHD · UniProt A0A0D6GS23
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