MolNFT v1 · #67538 · protein
Structure of the measles virus hemagglutinin bound to the CD46 receptor
3INB · Hemagglutinin glycoprotein: “Structure of the measles virus hemagglutinin bound to the CD46 receptor”. X-ray diffraction, 2 ligands (NAG, SO4), 17 pockets (best druggability 0.69). MolNFT v1 #67538 on GenesisL1: 3D structure…
- PDB
- 3INB
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin glycoprotein; Membrane cofactor protein
- UniProt
- P08362, P15529
- Ligands
- NAG, SO4
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin glycoprotein | protein | 389 | 7% helix, 48% strand | P08362 |
| B | Hemagglutinin glycoprotein | protein | 403 | 7% helix, 49% strand | P08362 |
| C, D | Membrane cofactor protein | protein | 126 | 0% helix, 20% strand | P15529 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.69 | 0.80 | 66 | empty |
| 2 | 712 | 0.69 | 0.76 | 84 | empty |
| 3 | 284 | 0.68 | 0.83 | 49 | empty |
| 4 | 281 | 0.68 | 0.83 | 48 | empty |
| 5 | 232 | 0.62 | 0.82 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1116 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1107 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3INB · Structure of the measles virus hemagglutinin bound to the CD46 receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P15529 · AlphaFold monomer V2.0 prediction for membrane cofactor protein (P15529) · a predicted model of the same protein · chain C against A, TM-score 0.82
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 P08362
- Every structure of UniProt P15529
- Elsewhere: RCSB PDB 3INB · PDBe 3INB · UniProt P08362 · UniProt P15529
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