MolNFT v1 · #19273 · protein
N-terminal domain of sialoadhesin (mouse) in complex with 3'SIALYLLACTOSE
1QFO · Protein (sialoadhesin): “N-terminal domain of sialoadhesin (mouse) in complex with 3'SIALYLLACTOSE”. X-ray diffraction, 3 ligands (SIA, GLC, GAL), 4 pockets (best druggability 0.47). MolNFT v1 #19273 on GenesisL1: 3D structure…
- PDB
- 1QFO
- Type
- protein
- Length
- 345 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (sialoadhesin)
- Ligands
- SIA, GLC, GAL
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (sialoadhesin) | protein | 115 | 8% helix, 43% strand | — |
| B | Protein (sialoadhesin) | protein | 116 | 8% helix, 43% strand | — |
| C | Protein (sialoadhesin) | protein | 114 | 11% helix, 44% strand | — |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.47 | 0.75 | 28 | empty |
| 2 | 132 | 0.39 | 0.74 | 23 | empty |
| 3 | 91 | 0.34 | 0.74 | 18 | empty |
| 4 | 62 | 0.30 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 500 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 278 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1QFO · N-terminal domain of sialoadhesin (mouse) in complex with 3'SIALYLLACTOSE · 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
- Elsewhere: RCSB PDB 1QFO · PDBe 1QFO
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