MolNFT v1 · #38684 · protein
Crystallographic structure of digestive lysozyme 1 from musca domestica bound to chitotetraose at 1.92 a resolution
2H5Z: “Crystallographic structure of digestive lysozyme 1 from musca domestica bound to chitotetraose at 1.92 a…”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.32). MolNFT v1 #38684 on GenesisL1: 3D structure, binding…
- PDB
- 2H5Z
- 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
- NAG
- Pockets
- 1 · best druggability 0.32
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 501 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2H5Z · Crystallographic structure of digestive lysozyme 1 from Musca domestica bound to… · 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 2H5Z · PDBe 2H5Z · UniProt Q7YT16
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