MolNFT v1 · #169038 · protein
Crystal structure of anti-muscle specific kinase (musk) Fab, MUSK1A
6WYR · MUSK1A light chain: “Crystal structure of anti-muscle specific kinase (musk) Fab, MUSK1A”. X-ray diffraction, 2 ligands (NAG, BMA), 10 pockets (best druggability 0.73). MolNFT v1 #169038 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WYR
- Type
- protein
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUSK1A light chain; MUSK1A heavy chain
- Ligands
- NAG, BMA
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | MUSK1A light chain | protein | 213 | 6% helix, 53% strand | — |
| H | MUSK1A heavy chain | protein | 222 | 12% helix, 50% strand | — |
| M | MUSK1A light chain | protein | 212 | 8% helix, 51% strand | — |
| I | MUSK1A heavy chain | protein | 226 | 12% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, I
- BMA · beta-D-mannopyranose · sugar
- EDO · 1,2-ethanediol · additive · 16 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.73 | 0.77 | 100 | EDO |
| 2 | 787 | 0.72 | 0.78 | 80 | EDO |
| 3 | 140 | 0.48 | 0.78 | 26 | empty |
| 4 | 172 | 0.48 | 0.76 | 27 | empty |
| 5 | 58 | 0.47 | 0.85 | 25 | EDO |
Interfaces
6 interfaces between chains.
- L–H · 1910 Ų buried · 15 hydrogen bonds · protein-protein
- M–I · 1907 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 431 Ų buried · 6 hydrogen bonds · protein-protein
- H–M · 187 Ų buried · 1 hydrogen bond · protein-protein
- L–I · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 6WYR · Crystal structure of anti-Muscle Specific Kinase (MuSK) Fab, MuSK1A · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 6WYR · PDBe 6WYR
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