MolNFT v1 · #65356 · protein
T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity-- pyridine binding
3GUP: “T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity-- pyridine binding”. X-ray diffraction, 4 ligands (0PY, MG, CL), 4 pockets (best druggability 0.77). MolNFT v1 #65356 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3GUP
- 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
- 0PY, MG, CL, CO3
- Pockets
- 4 · best druggability 0.77
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
- 0PY · pyridine · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.77 | 0.96 | 24 | MG, 0PY |
| 2 | 129 | 0.48 | 0.79 | 26 | empty |
| 3 | 113 | 0.47 | 0.79 | 23 | empty |
| 4 | 114 | 0.44 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, artifact).
Compared structures
- 3GUP · T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine 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 3GUP · PDBe 3GUP · UniProt P00720
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