Research workbench
T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--P- xylene binding
Analyse T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--P- xylene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GUM
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- P00720
- Ligands
- PXY, CA, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme (EC 3.2.1.17) | protein | 162 | 64% helix, 9% strand | P00720 |
Ligands and binding sites
- PXY · Para-xylene · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.80 | 0.96 | 27 | CA |
| 2 | 51 | 0.71 | 0.98 | 15 | PXY |
| 3 | 144 | 0.55 | 0.81 | 23 | empty |
| 4 | 134 | 0.52 | 0.80 | 24 | empty |
| 5 | 55 | 0.32 | 0.77 | 13 | CL |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, artifact).
Compared structures
- 3GUM · T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--p-xylene binding · 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 3GUM · PDBe 3GUM · UniProt P00720
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