MolNFT v1 · #36620 · protein
The crystallographic structure of the digestive lysozyme 1 from musca domestica at 1.90 ang.
2FBD: “The crystallographic structure of the digestive lysozyme 1 from musca domestica at 1.90 ang.”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.33). MolNFT v1 #36620 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2FBD
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme 1
- EC
- 3.2.1.17
- UniProt
- Q7YT16
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysozyme 1 (EC 3.2.1.17) | protein | 122 | 44% helix, 7% strand | Q7YT16 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.33 | 0.77 | 14 | PEG |
| 2 | 51 | 0.30 | 0.76 | 16 | PEG |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2FBD · The crystallographic structure of the digestive lysozyme 1 from Musca domestica at 1.90… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7YT16 · AlphaFold monomer V2.0 prediction for lysozyme 1 (Q7YT16) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q7YT16
- Elsewhere: RCSB PDB 2FBD · PDBe 2FBD · UniProt Q7YT16
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