MolNFT v1 · #110143 · protein
Antibody hemagglutinin complexes
4XNQ · H5.3 light chain: “Antibody hemagglutinin complexes”. X-ray diffraction, 2 ligands (NAG, FUC), 12 pockets (best druggability 0.70). MolNFT v1 #110143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XNQ
- Type
- protein
- Length
- 1,249 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H5.3 light chain; H5.3 heavy chain; Influenza H5 ha head domain vietnam rdt mutations
- UniProt
- H8PCX0
- Ligands
- NAG, FUC
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | H5.3 light chain | protein | 208 | 8% helix, 51% strand | — |
| B, H | H5.3 heavy chain | protein | 217 | 7% helix, 55% strand | — |
| D | Influenza H5 ha head domain vietnam rdt mutations | protein | 202 | 13% helix, 43% strand | H8PCX0 |
| C | Influenza H5 ha head domain vietnam rdt mutations | protein | 197 | 13% helix, 43% strand | H8PCX0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.70 | 0.77 | 76 | empty |
| 2 | 669 | 0.68 | 0.76 | 58 | empty |
| 3 | 638 | 0.65 | 0.75 | 60 | empty |
| 4 | 52 | 0.46 | 0.84 | 16 | empty |
| 5 | 106 | 0.41 | 0.77 | 22 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1918 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1826 Ų buried · 17 hydrogen bonds · protein-protein
- D–C · 740 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 545 Ų buried · 7 hydrogen bonds · protein-protein
- H–C · 528 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XNQ · Antibody hemagglutinin Complexes · the same entry in another collection · chain H against H, 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 H8PCX0
- Elsewhere: RCSB PDB 4XNQ · PDBe 4XNQ · UniProt H8PCX0
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