MolNFT v1 · #110140 · protein
Antibody influenza H5 complex
4XNM · H5.3 Fab light chain: “Antibody influenza H5 complex”. X-ray diffraction, 2 ligands (NAG, FUC), 15 pockets (best druggability 0.73). MolNFT v1 #110140 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XNM
- Type
- protein
- Length
- 1,255 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H5.3 Fab light chain; H5.3 Fab heavy chain; Hemagglutinin
- UniProt
- H8PCX0
- Ligands
- NAG, FUC
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | H5.3 Fab light chain | protein | 208 | 8% helix, 51% strand | — |
| H | H5.3 Fab heavy chain | protein | 217 | 6% helix, 53% strand | — |
| B | H5.3 Fab heavy chain | protein | 216 | 6% helix, 53% strand | — |
| C | Hemagglutinin | protein | 196 | 12% helix, 40% strand | H8PCX0 |
| D | Hemagglutinin | protein | 210 | 11% helix, 39% 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
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.73 | 0.78 | 86 | empty |
| 2 | 642 | 0.67 | 0.76 | 58 | empty |
| 3 | 653 | 0.66 | 0.76 | 62 | empty |
| 4 | 230 | 0.49 | 0.75 | 36 | empty |
| 5 | 178 | 0.48 | 0.76 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1924 Ų buried · 20 hydrogen bonds · protein-protein
- L–H · 1835 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 752 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 590 Ų buried · 9 hydrogen bonds · protein-protein
- H–C · 558 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XNM · Antibody Influenza H5 Complex · the same entry in another collection · chain L against L, 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 4XNM · PDBe 4XNM · UniProt H8PCX0
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