MolNFT v1 · #88997 · protein
Lysozyme trimer
4DC4 · Lysozyme C: “Lysozyme trimer”. X-ray diffraction, 2 ligands (NA, CL), 5 pockets (best druggability 0.56). MolNFT v1 #88997 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DC4
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- NA, CL
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.56 | 0.75 | 37 | GOL |
| 2 | 81 | 0.43 | 0.80 | 14 | NA |
| 3 | 59 | 0.34 | 0.77 | 17 | GOL |
| 4 | 68 | 0.31 | 0.75 | 16 | empty |
| 5 | 51 | 0.25 | 0.73 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 387 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 373 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4DC4 · Lysozyme Trimer · 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 P00698
- Elsewhere: RCSB PDB 4DC4 · PDBe 4DC4 · UniProt P00698
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.