MolNFT v1 · #156994 · protein
Crystal structure of hemagglutinin from H1N1 influenza a virus A/DENVER/57 bound to the C05 antibody
6ML8: “Crystal structure of hemagglutinin from H1N1 influenza a virus A/DENVER/57 bound to the C05 antibody”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 8 pockets (best druggability 0.63). MolNFT v1 #156994 on GenesisL1: 3D structure…
- PDB
- 6ML8
- Type
- protein
- Length
- 917 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; C05 antibody Fab heavy chain; C05 antibody Fab light chain
- UniProt
- Q2IBI1
- Ligands
- NAG, BMA, MAN
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 321 | 8% helix, 39% strand | Q2IBI1 |
| B | Hemagglutinin | protein | 157 | 51% helix, 11% strand | Q2IBI1 |
| H | C05 antibody Fab heavy chain | protein | 227 | 8% helix, 48% strand | — |
| L | C05 antibody Fab light chain | protein | 212 | 5% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.63 | 0.87 | 27 | empty |
| 2 | 143 | 0.57 | 0.83 | 22 | empty |
| 3 | 400 | 0.55 | 0.74 | 46 | empty |
| 4 | 217 | 0.54 | 0.78 | 37 | empty |
| 5 | 124 | 0.52 | 0.81 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2593 Ų buried · 36 hydrogen bonds · protein-protein
- H–L · 1713 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 775 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ML8 · Crystal structure of hemagglutinin from H1N1 Influenza A virus A/Denver/57 bound to the… · the same entry in another collection · chain B against B, 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
- Every structure of UniProt Q2IBI1
- Elsewhere: RCSB PDB 6ML8 · PDBe 6ML8 · UniProt Q2IBI1
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