Research workbench
Crystal structure of the complex of buffalo secretory glycoprotein with tetrasaccharide at 2.8A resolution
Analyse Crystal structure of the complex of buffalo secretory glycoprotein with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QF8
- Type
- protein
- Length
- 361 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3-like protein 1
- UniProt
- Q7YS85
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3-like protein 1 | protein | 361 | 36% helix, 23% strand | Q7YS85 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.64 | 0.78 | 49 | NAG |
| 2 | 126 | 0.54 | 0.82 | 22 | empty |
| 3 | 67 | 0.37 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2QF8 · Crystal structure of the complex of Buffalo Secretory Glycoprotein with tetrasaccharide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7YS85 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (Q7YS85) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7YS85
- Elsewhere: RCSB PDB 2QF8 · PDBe 2QF8 · UniProt Q7YS85
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