Research workbench
Cocrystal of an rsl-N23H and sulfonato-THIACALIX[4]ARENE - zinc complex
Analyse Cocrystal of an rsl-N23H and sulfonato-THIACALIX[4]ARENE - zinc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PR5
- Type
- protein
- Length
- 1,071 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin protein
- UniProt
- A0A0S4TLR1
- Ligands
- BDF, 80M, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 67% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, J | Fucose-binding lectin protein | protein | 89 | 0% helix, 67% strand | A0A0S4TLR1 |
| F, H, I, K | Fucose-binding lectin protein | protein | 90 | 0% helix, 67% strand | A0A0S4TLR1 |
| L | Fucose-binding lectin protein | protein | 88 | 0% helix, 68% strand | A0A0S4TLR1 |
Ligands and binding sites
- BDF · beta-D-fructopyranose · ligand · 23 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- 80M · sulfonato-thiacalix[4]arene · ligand · chains G, I, K, L
- ZN · Zinc ion · metal · 7 copies · chains A, F, B, L, D, G, C, H, I, E, J, K
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.76 | 0.80 | 77 | empty |
| 2 | 843 | 0.76 | 0.80 | 78 | empty |
| 3 | 798 | 0.75 | 0.80 | 79 | empty |
| 4 | 824 | 0.75 | 0.80 | 78 | empty |
| 5 | 413 | 0.62 | 0.77 | 37 | empty |
Interfaces
32 interfaces between chains.
- J–K · 810 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 804 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 796 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 775 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 771 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7PR5 · Cocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc complex · 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 7PR5 · PDBe 7PR5 · UniProt A0A0S4TLR1
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