MolNFT v1 · #34927 · protein
Crystals of peanut lectin grown in the presence of gal- alpha-1,3-gal-beta-1,4-gal
2DVF · Galactose-binding lectin: “Crystals of peanut lectin grown in the presence of gal- alpha-1,3-gal-beta-1,4-gal”. X-ray diffraction, 3 ligands (CA, MN, SO4), 5 pockets (best druggability 0.78). MolNFT v1 #34927 on GenesisL1: 3D…
- PDB
- 2DVF
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-binding lectin
- UniProt
- P02872
- Ligands
- CA, MN, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Galactose-binding lectin | protein | 232 | 4% helix, 49% strand | P02872 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.78 | 0.81 | 107 | empty |
| 2 | 146 | 0.47 | 0.77 | 28 | empty |
| 3 | 132 | 0.44 | 0.77 | 23 | empty |
| 4 | 129 | 0.42 | 0.76 | 23 | empty |
| 5 | 105 | 0.39 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 970 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 731 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 602 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 67 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2DVF · Crystals of peanut lectin grown in the presence of GAL-ALPHA-1,3-GAL-BETA-1,4-GAL · the same entry in another collection · chain A against A, TM-score 1.00
- P02872 · AlphaFold monomer V2.0 prediction for galactose-binding lectin (P02872) · a predicted model of the same protein · 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 P02872
- Elsewhere: RCSB PDB 2DVF · PDBe 2DVF · UniProt P02872
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