MolNFT v1 · #38099 · protein
Metal-free (apo) P. angolensis seed lectin in complex with glcnac- BETA(1-2)MAN
2GMP: “Metal-free (apo) P. angolensis seed lectin in complex with glcnac- BETA(1-2)MAN”. X-ray diffraction, 3 ligands (MAN, NAG, SO4), 2 pockets (best druggability 0.32). MolNFT v1 #38099 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GMP
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- Q8GSD2
- Ligands
- MAN, NAG, SO4
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin | protein | 228 | 3% helix, 51% strand | Q8GSD2 |
| B | Lectin | protein | 233 | 3% helix, 48% strand | Q8GSD2 |
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
- SO4 · Sulfate ion · ion · chains A
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 | 54 | 0.32 | 0.76 | 15 | empty |
| 2 | 55 | 0.31 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 877 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cyclization).
Compared structures
- 2GMP · Metal-free (apo) P. angolensis seed lectin in complex with GlcNAC-beta(1-2)Man · 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 2GMP · PDBe 2GMP · UniProt Q8GSD2
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