MolNFT v1 · #82366 · protein
Protease-resistant mutant form of human galectin-8 in complex with sialyllactose and lactose
3VKM: “Protease-resistant mutant form of human galectin-8 in complex with sialyllactose and lactose”. X-ray diffraction, 3 ligands (BGC, GAL, SIA), 5 pockets (best druggability 0.83). MolNFT v1 #82366 on GenesisL1: 3D structure, binding…
- PDB
- 3VKM
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galectin-8
- UniProt
- O00214
- Ligands
- BGC, GAL, SIA
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Galectin-8 | protein | 291 | 3% helix, 55% strand | O00214 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
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 | 1057 | 0.83 | 0.84 | 107 | EDO |
| 2 | 97 | 0.49 | 0.81 | 23 | empty |
| 3 | 60 | 0.44 | 0.83 | 14 | empty |
| 4 | 74 | 0.35 | 0.76 | 15 | empty |
| 5 | 54 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3VKM · Protease-resistant mutant form of Human Galectin-8 in complex with sialyllactose and… · the same entry in another collection · chain A against A, TM-score 1.00
- O00214 · AlphaFold monomer V2.0 prediction for galectin-8 (O00214) · a predicted model of the same protein · chain A against A, TM-score 0.56
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 O00214
- Elsewhere: RCSB PDB 3VKM · PDBe 3VKM · UniProt O00214
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