MolNFT v1 · #168390 · protein
Crystal structure of broadly neutralizing antibody 3I14-D93N mutant bound to the influenza a H3 hemagglutinin
6WEZ: “Crystal structure of broadly neutralizing antibody 3I14-D93N mutant bound to the influenza a H3 hemagglutinin”. X-ray diffraction, 2 ligands (NAG, BMA), 10 pockets (best druggability 0.71). MolNFT v1 #168390 on GenesisL1: 3D…
- PDB
- 6WEZ
- 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
- 10 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 317 | 10% helix, 39% strand | A0A5P1MU07 |
| B | Hemagglutinin | protein | 163 | 55% helix, 13% strand | A0A2P1E3C0 |
| H | Heavy chain | protein | 223 | 5% helix, 45% strand | — |
| L | Light chain | protein | 213 | 4% helix, 45% 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 · 3 copies
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.71 | 0.83 | 53 | empty |
| 2 | 460 | 0.60 | 0.75 | 47 | empty |
| 3 | 51 | 0.57 | 0.91 | 18 | empty |
| 4 | 97 | 0.56 | 0.85 | 18 | empty |
| 5 | 136 | 0.56 | 0.82 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3018 Ų buried · 45 hydrogen bonds · protein-protein
- H–L · 1785 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 477 Ų buried · 5 hydrogen bonds · protein-protein
- B–L · 292 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6WEZ · Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant Bound to the… · 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 6WEZ · PDBe 6WEZ · UniProt A0A5P1MU07 · UniProt A0A2P1E3C0
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