MolNFT v1 · #148485 · protein
Crystal structure of dimethylated rsl, cucurbituril-free form
6F7Y · Fucose-binding lectin protein: “Crystal structure of dimethylated rsl, cucurbituril-free form”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #148485 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F7Y
- Type
- protein
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein
- UniProt
- A0A0S4TLR1
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucose-binding lectin protein | protein | 90 | 0% helix, 67% strand | A0A0S4TLR1 |
| B, C, D | Fucose-binding lectin protein | protein | 89 | 0% helix, 63% strand | A0A0S4TLR1 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.75 | 0.82 | 69 | empty |
| 2 | 281 | 0.66 | 0.82 | 46 | GOL |
| 3 | 113 | 0.39 | 0.75 | 20 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 774 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 773 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 770 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 680 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (methylation, nonstandard).
Compared structures
- 6F7Y · Crystal structure of dimethylated RSL, cucurbituril-free form · the same entry in another collection · 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 A0A0S4TLR1
- Elsewhere: RCSB PDB 6F7Y · PDBe 6F7Y · UniProt A0A0S4TLR1
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