MolNFT v1 · #172188 · protein
Crystal structure of dimethylated rsl-N23H/G68H (rsl-B6) in complex with CUCURBIT[7]URIL and zinc
6ZUK · Fucose-binding lectin protein: “Crystal structure of dimethylated rsl-N23H/G68H (rsl-B6) in complex with CUCURBIT[7]URIL and zinc”. X-ray diffraction, 4 ligands (QQ7, SNM, ZN), 8 pockets (best druggability 0.79). MolNFT v1 #172188…
- PDB
- 6ZUK
- Type
- protein
- Length
- 522 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein
- UniProt
- A0A0S4TLR1
- Ligands
- QQ7, SNM, ZN, NA
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 69% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Fucose-binding lectin protein | protein | 87 | 0% helix, 69% strand | A0A0S4TLR1 |
Ligands and binding sites
- QQ7 · cucurbit[7]uril · ligand · 5 copies · chains A, B, C, D, E
- SNM · N,N-dimethyl-L-serine · ligand · 3 copies · chains A, E, B, F, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, E, B, F, C, D
- NA · Sodium ion · metal
- GOL · Glycerol · additive · 10 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.79 | 0.82 | 81 | SNM |
| 2 | 352 | 0.77 | 0.88 | 49 | empty |
| 3 | 516 | 0.76 | 0.84 | 51 | empty |
| 4 | 84 | 0.36 | 0.76 | 17 | empty |
| 5 | 65 | 0.31 | 0.75 | 16 | empty |
Interfaces
12 interfaces between chains.
- D–E · 679 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 669 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 667 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 665 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (methylation).
Compared structures
- 6ZUK · Crystal structure of dimethylated RSL-N23H/G68H (RSL-B6) in complex with cucurbit[7]uril… · 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 6ZUK · PDBe 6ZUK · UniProt A0A0S4TLR1
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