MolNFT v1 · #61494 · protein
Iodopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant (seleno version)
3DN8: “Iodopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant (seleno version)”. X-ray diffraction, 3 ligands (IBF, PO4, CL), 2 pockets (best druggability 0.71). MolNFT v1 #61494 on GenesisL1: 3D structure…
- PDB
- 3DN8
- Type
- protein
- Length
- 162 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- IBF, PO4, CL
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 162 | 64% helix, 8% strand | P00720 |
Ligands and binding sites
- IBF · 1,2,3,4,5-pentafluoro-6-iodobenzene · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- HED · 2-hydroxyethyl disulfide · additive · 3 copies · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.97 | 16 | IBF |
| 2 | 243 | 0.53 | 0.76 | 31 | HED |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3DN8 · Iodopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant… · 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 P00720
- Elsewhere: RCSB PDB 3DN8 · PDBe 3DN8 · UniProt P00720
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