MolNFT v1 · #53903 · protein
The structure of a family GH25 lysozyme from aspergillus fumigatus
2X8R · Glycosyl hydrolase: “The structure of a family GH25 lysozyme from aspergillus fumigatus”. X-ray diffraction, 1 ligand (CL), 17 pockets (best druggability 0.83). MolNFT v1 #53903 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2X8R
- Type
- protein
- Length
- 1,257 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase
- EC
- 3.2.1.17
- UniProt
- A4DA29
- Ligands
- CL
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Glycosyl hydrolase (EC 3.2.1.17) | protein | 209 | 31% helix, 23% strand | A4DA29 |
| B, C, E | Glycosyl hydrolase (EC 3.2.1.17) | protein | 210 | 31% helix, 22% strand | A4DA29 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.83 | 0.84 | 118 | empty |
| 2 | 1018 | 0.80 | 0.82 | 86 | CL |
| 3 | 401 | 0.75 | 0.85 | 37 | empty |
| 4 | 560 | 0.66 | 0.77 | 33 | empty |
| 5 | 268 | 0.58 | 0.79 | 26 | empty |
Interfaces
10 interfaces between chains.
- B–C · 643 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 350 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 346 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 247 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2X8R · The structure of a family GH25 lysozyme from Aspergillus fumigatus · 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 A4DA29
- Elsewhere: RCSB PDB 2X8R · PDBe 2X8R · UniProt A4DA29
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