Research workbench
Crystal structure of snake gourd seed lectin in complex with lactose
Analyse Crystal structure of snake gourd seed lectin in complex with lactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y97
- Type
- protein
- Length
- 511 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Seed lectin
- UniProt
- U3KRF8
- Ligands
- BGC, GAL, NAG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Seed lectin | protein | 41 | 44% helix, 34% strand | U3KRF8 |
| B | Seed lectin | protein | 206 | 38% helix, 24% strand | U3KRF8 |
| C | Seed lectin | protein | 264 | 8% helix, 42% strand | U3KRF8 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains C
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.79 | 0.97 | 27 | empty |
| 2 | 290 | 0.55 | 0.76 | 41 | empty |
| 3 | 251 | 0.55 | 0.77 | 34 | empty |
| 4 | 115 | 0.43 | 0.77 | 18 | empty |
| 5 | 59 | 0.31 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1729 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1724 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 199 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 U3KRF8
- Elsewhere: RCSB PDB 5Y97 · PDBe 5Y97 · UniProt U3KRF8
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