Research workbench
Iodopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant (seleno version)
Analyse Iodopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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