MolNFT v1 · #142443 · protein
Human antibody 32D6 Fab in complex with H1N1 influenza a virus HA1
6A4K · Hemagglutinin: “Human antibody 32D6 Fab in complex with H1N1 influenza a virus HA1”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.78). MolNFT v1 #142443 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6A4K
- Type
- protein
- Length
- 2,672 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Immunoglobulin Fab heavy chain; Immunoglobulin Fab light chain
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin | protein | 223 | 11% helix, 38% strand | — |
| H, I, J, K | Immunoglobulin Fab heavy chain | protein | 230 | 5% helix, 48% strand | — |
| L, M, N, O | Immunoglobulin Fab light chain | protein | 216 | 6% helix, 50% strand | — |
| B, D | Hemagglutinin | protein | 221 | 10% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.78 | 0.80 | 118 | ACT |
| 2 | 904 | 0.77 | 0.80 | 116 | CA, ACT |
| 3 | 72 | 0.65 | 0.92 | 24 | empty |
| 4 | 306 | 0.63 | 0.79 | 52 | empty |
| 5 | 295 | 0.61 | 0.79 | 39 | empty |
Interfaces
16 interfaces between chains.
- J–N · 1952 Ų buried · 14 hydrogen bonds · protein-protein
- K–O · 1907 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 1864 Ų buried · 16 hydrogen bonds · protein-protein
- I–M · 1814 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 617 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6A4K · Human antibody 32D6 Fab in complex with H1N1 influenza A virus HA1 · 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
- Elsewhere: RCSB PDB 6A4K · PDBe 6A4K
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