MolNFT v1 · #21156 · protein
Pterocarpus angolensis seed lectin (pal) with one binding site free and one binding site containing the disaccharide MAN(A1-3)MANME
1S1A: “Pterocarpus angolensis seed lectin (pal) with one binding site free and one binding site containing the…”. X-ray diffraction, 4 ligands (MMA, MAN, MN), 2 pockets (best druggability 0.34). MolNFT v1 #21156 on GenesisL1: 3D structure…
- PDB
- 1S1A
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- Q8GSD2
- Ligands
- MMA, MAN, MN, CA
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 240 | 5% helix, 47% strand | Q8GSD2 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.34 | 0.77 | 16 | empty |
| 2 | 60 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 921 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cyclization).
Compared structures
- 1S1A · Pterocarpus angolensis seed lectin (PAL) with one binding site free and one binding site… · 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 Q8GSD2
- Elsewhere: RCSB PDB 1S1A · PDBe 1S1A · UniProt Q8GSD2
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