MolNFT v1 · #109188 · protein
Crystal structure of a recombinant vatairea macrocarpa seed lectin complexed with lactose
4WV8: “Crystal structure of a recombinant vatairea macrocarpa seed lectin complexed with lactose”. X-ray diffraction, 4 ligands (GLC, GAL, CA), 4 pockets (best druggability 0.77). MolNFT v1 #109188 on GenesisL1: 3D structure, binding sites…
- PDB
- 4WV8
- Type
- protein
- Length
- 950 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seed lectin
- UniProt
- P81371
- Ligands
- GLC, GAL, CA, MN
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seed lectin | protein | 236 | 6% helix, 47% strand | P81371 |
| B | Seed lectin | protein | 237 | 4% helix, 46% strand | P81371 |
| C | Seed lectin | protein | 238 | 3% helix, 47% strand | P81371 |
| D | Seed lectin | protein | 239 | 3% helix, 46% strand | P81371 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.77 | 0.79 | 89 | empty |
| 2 | 1083 | 0.76 | 0.79 | 97 | empty |
| 3 | 52 | 0.38 | 0.81 | 16 | empty |
| 4 | 54 | 0.28 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1004 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 819 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 782 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 61 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4WV8 · Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with lactose · the same entry in another collection · chain D against D, TM-score 1.00
- P81371 · AlphaFold monomer V2.0 prediction for seed lectin (P81371) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P81371
- Elsewhere: RCSB PDB 4WV8 · PDBe 4WV8 · UniProt P81371
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.