Research workbench
Crystal structure of dimethylated rsl in complex with CUCURBIT[7]URIL and zinc
Analyse Crystal structure of dimethylated rsl in complex with CUCURBIT[7]URIL and zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZUL
- Type
- protein
- Length
- 539 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein
- UniProt
- A0A0S4TLR1
- Ligands
- QQ7, NA, ZN
- Pockets
- 2 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Fucose-binding lectin protein | protein | 90 | 0% helix, 64% strand | A0A0S4TLR1 |
| B | Fucose-binding lectin protein | protein | 89 | 0% helix, 67% strand | A0A0S4TLR1 |
Ligands and binding sites
- QQ7 · cucurbit[7]uril · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 4 copies
- ZN · Zinc ion · metal · 2 copies · chains A, F
- GOL · Glycerol · additive · 12 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.89 | 0.91 | 120 | empty |
| 2 | 120 | 0.41 | 0.76 | 27 | GOL |
Interfaces
13 interfaces between chains.
- C–E · 797 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 795 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 791 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 788 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 786 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (methylation, nonstandard).
Compared structures
- 6ZUL · Crystal structure of dimethylated RSL in complex with cucurbit[7]uril and zinc · 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 6ZUL · PDBe 6ZUL · UniProt A0A0S4TLR1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.