Research workbench
Hemagglutinin influenza a virus (A/OKUDA/1957(H2N2) bound with a neutralizing antibody
Analyse Hemagglutinin influenza a virus (A/OKUDA/1957(H2N2) bound with a neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DKJ
- Type
- protein
- Length
- 2,490 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Fv-clasp heavy chain; Fv-clasp light chain
- UniProt
- A0A0A7E4R0
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Hemagglutinin | protein | 498 | 24% helix, 24% strand | A0A0A7E4R0 |
| C, G, K | Fv-clasp heavy chain | protein | 173 | 28% helix, 29% strand | — |
| D, H, L | Fv-clasp light chain | protein | 159 | 26% helix, 23% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, D, E, H, I, L, C, G, K
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.82 | 0.83 | 94 | empty |
| 2 | 865 | 0.76 | 0.80 | 100 | NAG |
| 3 | 60 | 0.73 | 0.98 | 15 | empty |
| 4 | 553 | 0.72 | 0.80 | 67 | empty |
| 5 | 506 | 0.72 | 0.81 | 59 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2335 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 2325 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 2306 Ų buried · 9 hydrogen bonds · protein-protein
- E–I · 2093 Ų buried · 18 hydrogen bonds · protein-protein
- A–I · 2085 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7DKJ · Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody · 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 A0A0A7E4R0
- Elsewhere: RCSB PDB 7DKJ · PDBe 7DKJ · UniProt A0A0A7E4R0
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