Research workbench
Pterocarpus angolensis lectin (pal) in complex with man-7D1
Analyse Pterocarpus angolensis lectin (pal) in complex with man-7D1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PHR
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- Q8GSD2
- Ligands
- MAN, BMA, MN, CA
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 240 | 4% helix, 48% strand | Q8GSD2 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · chains B
- 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 | 58 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cyclization).
Compared structures
- 2PHR · Pterocarpus angolensis lectin (PAL) in complex with Man-7D1 · 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 2PHR · PDBe 2PHR · UniProt Q8GSD2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.