Research workbench
T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity-- toluene binding
Analyse T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity-- toluene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GUK
- 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
- MBN, CA, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme (EC 3.2.1.17) | protein | 162 | 65% helix, 9% strand | P00720 |
Ligands and binding sites
- MBN · Toluene · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.78 | 0.95 | 29 | CA |
| 2 | 117 | 0.51 | 0.81 | 25 | empty |
| 3 | 129 | 0.50 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, artifact).
Compared structures
- 3GUK · T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--Toluene 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 3GUK · PDBe 3GUK · UniProt P00720
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