MolNFT v2 · #143212 · protein
Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region
6A0Z · Hemagglutinin,Envelope glycoprotein: “Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region”. X-ray diffraction at 2.329, 1 ligand (NAG), 6 pockets (best druggability 0.61).…
- PDB
- 6A0Z
- Type
- protein
- Length
- 706 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.329
- Source
- Human immunodeficiency virus 1; Influenza A virus; Mus musculus
- Molecule
- Hemagglutinin,Envelope glycoprotein; Antibody 13D4, Fab Heavy Chain; Antibody 13D4, Fab…
- UniProt
- Q45ZR9, M1E1E4
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.329 · 3 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin,Envelope glycoprotein | protein | 270 | 11% helix, 39% strand | Q45ZR9, M1E1E4 |
| H | Antibody 13D4, Fab Heavy Chain | protein | 224 | 5% helix, 50% strand | — |
| L | Antibody 13D4, Fab Light Chain | protein | 212 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.61 | 0.74 | 72 | empty |
| 2 | 145 | 0.45 | 0.76 | 24 | empty |
| 3 | 52 | 0.38 | 0.81 | 19 | empty |
| 4 | 72 | 0.34 | 0.76 | 17 | empty |
| 5 | 77 | 0.33 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1922 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 752 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 249 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 6A0Z · Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza… · 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
- Every structure of UniProt Q45ZR9
- Every structure of UniProt M1E1E4
- Elsewhere: RCSB PDB 6A0Z · PDBe 6A0Z · UniProt Q45ZR9 · UniProt M1E1E4
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