MolNFT v1 · #127434 · protein
Human JAGGED2 C2-EGF2
5MWF · Protein jagged-2: “Human JAGGED2 C2-EGF2”. X-ray diffraction, 5 ligands (NAG, FUC, BMA), 11 pockets (best druggability 0.73). MolNFT v1 #127434 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MWF
- Type
- protein
- Length
- 1,592 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein jagged-2
- UniProt
- Q9Y219
- Ligands
- NAG, FUC, BMA, CA, CL
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 2% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein jagged-2 | protein | 276 | 4% helix, 38% strand | Q9Y219 |
| B | Protein jagged-2 | protein | 275 | 4% helix, 38% strand | Q9Y219 |
| C | Protein jagged-2 | protein | 262 | 1% helix, 41% strand | Q9Y219 |
| D | Protein jagged-2 | protein | 266 | 2% helix, 38% strand | Q9Y219 |
| E | Protein jagged-2 | protein | 260 | 0% helix, 41% strand | Q9Y219 |
| F | Protein jagged-2 | protein | 253 | 2% helix, 41% strand | Q9Y219 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · 17 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.73 | 0.77 | 83 | empty |
| 2 | 810 | 0.72 | 0.77 | 85 | empty |
| 3 | 204 | 0.49 | 0.76 | 25 | empty |
| 4 | 215 | 0.47 | 0.74 | 28 | empty |
| 5 | 180 | 0.44 | 0.74 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–E · 772 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 738 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 656 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 480 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 6 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 Q9Y219
- Elsewhere: RCSB PDB 5MWF · PDBe 5MWF · UniProt Q9Y219
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