Research workbench
Crystal structure of dimethylated rsl - CUCURBIT[7]URIL complex, F432 form
Analyse Crystal structure of dimethylated rsl - CUCURBIT[7]URIL complex, F432 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F7X
- Type
- protein
- Length
- 270 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein
- UniProt
- A0A0S4TLR1
- Ligands
- MFU, QQ7
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 68% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fucose-binding lectin protein | protein | 90 | 0% helix, 68% strand | A0A0S4TLR1 |
Ligands and binding sites
- MFU · methyl alpha-L-fucopyranoside · ligand · 6 copies · chains A, C, B
- QQ7 · cucurbit[7]uril · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.74 | 0.82 | 49 | empty |
| 2 | 281 | 0.53 | 0.76 | 33 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 786 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 779 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 776 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (methylation, nonstandard).
Compared structures
- 6F7X · Crystal structure of dimethylated RSL - cucurbit[7]uril complex, F432 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 6F7X · PDBe 6F7X · UniProt A0A0S4TLR1
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