MolNFT v1 · #139429 · protein
Crystal structure of orysata lectin in complex with biantennary N- glycan
5XFH · Salt stress-induced protein: “Crystal structure of orysata lectin in complex with biantennary N- glycan”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 1 pocket (best druggability 0.48). MolNFT v1 #139429 on GenesisL1: 3D structure…
- PDB
- 5XFH
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Salt stress-induced protein
- UniProt
- Q0JMY8
- Ligands
- MAN, NAG, BMA, GAL
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 68% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Salt stress-induced protein | protein | 141 | 0% helix, 69% strand | Q0JMY8 |
| B | Salt stress-induced protein | protein | 144 | 0% helix, 67% strand | Q0JMY8 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A
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 | 112 | 0.48 | 0.80 | 13 | BMA |
Interfaces
1 interface between chains.
- A–B · 262 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XFH · Crystal structure of Orysata lectin in complex with biantennary N-glycan · the same entry in another collection · chain A against A, TM-score 1.00
- Q0JMY8 · AlphaFold monomer V2.0 prediction for salt stress-induced protein (Q0JMY8) · 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 Q0JMY8
- Elsewhere: RCSB PDB 5XFH · PDBe 5XFH · UniProt Q0JMY8
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