Research workbench
Crystal structure of kl with an agonist Fab
Analyse Crystal structure of kl with an agonist Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WI9
- Type
- protein
- Length
- 1,680 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-klotho; 39F7 Fab light chain; 39F7 Fab heavy chain
- UniProt
- Q86Z14
- Ligands
- NAG, SO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-klotho | protein | 425 | 47% helix, 16% strand | Q86Z14 |
| L | 39F7 Fab light chain | protein | 188 | 6% helix, 45% strand | — |
| H | 39F7 Fab heavy chain | protein | 217 | 6% helix, 51% strand | — |
| E | 39F7 Fab light chain | protein | 212 | 7% helix, 51% strand | — |
| F | 39F7 Fab heavy chain | protein | 213 | 3% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, L, H
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.83 | 0.94 | 43 | EDO |
| 2 | 262 | 0.81 | 0.93 | 36 | empty |
| 3 | 60 | 0.73 | 0.99 | 20 | EDO |
| 4 | 59 | 0.70 | 0.97 | 19 | empty |
| 5 | 52 | 0.68 | 0.97 | 20 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1750 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1737 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 744 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 722 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 Q86Z14
- Elsewhere: RCSB PDB 5WI9 · PDBe 5WI9 · UniProt Q86Z14
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.