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The crystal structure of the 58KD vegetative lectin from the tropical legume dolichos biflorus
Analyse The crystal structure of the 58KD vegetative lectin from the tropical legume… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G7Y
- Type
- protein
- Length
- 1,496 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- STEM/LEAF lectin DB58
- UniProt
- P19588
- Ligands
- NAG, FUC, FUL, CA, MN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | STEM/LEAF lectin DB58 | protein | 251 | 9% helix, 43% strand | P19588 |
| B, F | STEM/LEAF lectin DB58 | protein | 246 | 8% helix, 44% strand | P19588 |
| D | STEM/LEAF lectin DB58 | protein | 253 | 8% helix, 43% strand | P19588 |
| E | STEM/LEAF lectin DB58 | protein | 249 | 8% helix, 43% strand | P19588 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C, E
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- FUL · beta-L-fucopyranose · sugar
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.84 | 0.88 | 122 | empty |
| 2 | 308 | 0.82 | 0.93 | 53 | empty |
| 3 | 283 | 0.79 | 0.91 | 56 | empty |
| 4 | 80 | 0.70 | 0.95 | 27 | empty |
| 5 | 272 | 0.60 | 0.79 | 48 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1474 Ų buried · 83 hydrogen bonds · protein-protein
- A–C · 1463 Ų buried · 88 hydrogen bonds · protein-protein
- E–F · 1456 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 927 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 749 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 1G7Y · The crystal structure of the 58KD vegetative lectin from the tropical legume dolichos… · the same entry in another collection · chain F against F, TM-score 1.00
- P19588 · AlphaFold monomer V2.0 prediction for lectin DB58 (P19588) · a predicted model of the same protein · chain D 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 P19588
- Elsewhere: RCSB PDB 1G7Y · PDBe 1G7Y · UniProt P19588
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