Research workbench
Iodobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant (seleno version)
Analyse Iodobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DNA
- 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
- PIH, PO4, CL
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 162 | 65% helix, 8% strand | P00720 |
Ligands and binding sites
- PIH · 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 | 57 | 0.73 | 0.98 | 17 | PIH |
| 2 | 246 | 0.54 | 0.76 | 29 | HED |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3DNA · Iodobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant (seleno version) · 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 3DNA · PDBe 3DNA · UniProt P00720
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