Research workbench
Dimethylated fusion protein of rsl and trimeric coiled coil in complex with CUCURBIT[7]URIL
Analyse Dimethylated fusion protein of rsl and trimeric coiled coil in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S99
- Type
- protein
- Length
- 672 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4DZN-RSL,FUCOSE-binding lectin protein
- UniProt
- A0A0S4TLR1
- Ligands
- QQ7, SNM, BMA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 4DZN-RSL,FUCOSE-binding lectin protein | protein | 112 | 20% helix, 51% strand | A0A0S4TLR1 |
Ligands and binding sites
- QQ7 · cucurbit[7]uril · ligand · 6 copies · chains A, B, C, D, E, F
- SNM · N,N-dimethyl-L-serine · ligand · 6 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.83 | 0.84 | 97 | empty |
| 2 | 816 | 0.72 | 0.77 | 72 | empty |
| 3 | 557 | 0.67 | 0.78 | 43 | empty |
| 4 | 50 | 0.22 | 0.71 | 16 | empty |
Interfaces
12 interfaces between chains.
- B–C · 880 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 854 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 831 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 804 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 797 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified, 6 covalent (methylation, covalent ligand).
Compared structures
- 6S99 · Dimethylated fusion protein of RSL and trimeric coiled coil in complex with… · the same entry in another collection · chain B against B, 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 6S99 · PDBe 6S99 · UniProt A0A0S4TLR1
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