MolNFT v1 · #168391 · protein
Crystal structure of broadly neutralizing antibody 3I14 bound to the influenza a H3 hemagglutinin
6WF0: “Crystal structure of broadly neutralizing antibody 3I14 bound to the influenza a H3 hemagglutinin”. X-ray diffraction, 2 ligands (NAG, BMA), 11 pockets (best druggability 0.69). MolNFT v1 #168391 on GenesisL1: 3D structure, binding…
- PDB
- 6WF0
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Heavy chain; Light chain
- UniProt
- A0A5P1MU07, A0A2P1E3C0
- Ligands
- NAG, BMA
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 317 | 8% helix, 38% strand | A0A5P1MU07 |
| B | Hemagglutinin | protein | 163 | 54% helix, 14% strand | A0A2P1E3C0 |
| H | Heavy chain | protein | 223 | 5% helix, 45% strand | — |
| L | Light chain | protein | 213 | 5% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, H
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.69 | 0.82 | 65 | empty |
| 2 | 557 | 0.62 | 0.75 | 53 | empty |
| 3 | 270 | 0.58 | 0.78 | 41 | empty |
| 4 | 112 | 0.52 | 0.82 | 28 | empty |
| 5 | 129 | 0.49 | 0.79 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3035 Ų buried · 44 hydrogen bonds · protein-protein
- H–L · 1740 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 506 Ų buried · 6 hydrogen bonds · protein-protein
- B–L · 289 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6WF0 · Crystal Structure of Broadly Neutralizing Antibody 3I14 Bound to the Influenza A H3… · 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 A0A5P1MU07
- Every structure of UniProt A0A2P1E3C0
- Elsewhere: RCSB PDB 6WF0 · PDBe 6WF0 · UniProt A0A5P1MU07 · UniProt A0A2P1E3C0
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