Research workbench
Crystal structure of dimethylated rslex in complex with CUCURBIT[7]URIL
Analyse Crystal structure of dimethylated rslex in complex with CUCURBIT[7]URIL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SU0
- Type
- protein
- Length
- 1,068 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein
- UniProt
- A0A0S4TLR1
- Ligands
- QQ7, MFU, NA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 85% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, I, J, K, M, N, O | Fucose-binding lectin protein | protein | 89 | 0% helix, 85% strand | A0A0S4TLR1 |
Ligands and binding sites
- QQ7 · cucurbit[7]uril · ligand · 12 copies · chains A, I, B, J, C, K, D, M, F, N, E, O
- MFU · methyl alpha-L-fucopyranoside · ligand · 12 copies · chains A, I, K, C, B, J, D, F, M, E, N, O
- NA · Sodium ion · metal · 6 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.78 | 0.85 | 92 | empty |
| 2 | 593 | 0.78 | 0.84 | 97 | empty |
| 3 | 118 | 0.38 | 0.74 | 39 | empty |
| 4 | 79 | 0.34 | 0.76 | 22 | empty |
| 5 | 51 | 0.25 | 0.74 | 26 | empty |
Interfaces
36 interfaces between chains.
- E–N · 1875 Ų buried · 316 hydrogen bonds · protein-protein
- D–N · 1867 Ų buried · 331 hydrogen bonds · protein-protein
- C–K · 1867 Ų buried · 316 hydrogen bonds · protein-protein
- A–K · 1858 Ų buried · 335 hydrogen bonds · protein-protein
- F–M · 1848 Ų buried · 321 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 12 disulfide (methylation, disulfide).
Compared structures
- 6SU0 · Crystal structure of dimethylated RSLex in complex with cucurbit[7]uril · 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 6SU0 · PDBe 6SU0 · UniProt A0A0S4TLR1
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