MolNFT v1 · #24597 · protein
Erythrina cristagalli lectin
1V00 · Lectin (ecl): “Erythrina cristagalli lectin”. X-ray diffraction, 4 ligands (BGC, GAL, MN), 3 pockets (best druggability 0.46). MolNFT v1 #24597 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1V00
- Type
- protein
- Length
- 958 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin (ecl)
- UniProt
- Q6YD91
- Ligands
- BGC, GAL, MN, CA
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lectin (ecl) | protein | 239 | 4% helix, 45% strand | Q6YD91 |
| B, C | Lectin (ecl) | protein | 240 | 4% helix, 45% strand | Q6YD91 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.46 | 0.76 | 29 | empty |
| 2 | 52 | 0.35 | 0.79 | 14 | empty |
| 3 | 52 | 0.34 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 839 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1V00 · Erythrina cristagalli lectin · 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 Q6YD91
- Elsewhere: RCSB PDB 1V00 · PDBe 1V00 · UniProt Q6YD91
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