Research workbench
Crystal structure of a subtype H18 hemagglutinin homologue from A/FLAT-faced BAT/PERU/033/2010 (H18N11)
Analyse Crystal structure of a subtype H18 hemagglutinin homologue from A/FLAT-faced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MC5
- Type
- protein
- Length
- 1,485 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG, FUC, MAN, BMA, FUL
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin | protein | 494 | 26% helix, 29% strand | — |
| C | Hemagglutinin | protein | 497 | 25% helix, 30% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.86 | 0.97 | 33 | empty |
| 2 | 850 | 0.85 | 0.87 | 77 | empty |
| 3 | 93 | 0.74 | 0.96 | 17 | empty |
| 4 | 132 | 0.72 | 0.92 | 28 | FUC |
| 5 | 142 | 0.71 | 0.91 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2073 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2066 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2052 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 4MC5 · Crystal structure of a subtype H18 hemagglutinin homologue from A/flat-faced… · 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
- Elsewhere: RCSB PDB 4MC5 · PDBe 4MC5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.