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Structure of the hemagglutinin complexed with 3SLN from a highly pathogenic H7N7 influenza virus
Analyse Structure of the hemagglutinin complexed with 3SLN from a highly pathogenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DJ7
- Type
- protein
- Length
- 1,458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q6VMK1
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 316 | 9% helix, 38% strand | Q6VMK1 |
| B | Hemagglutinin | protein | 170 | 54% helix, 12% strand | Q6VMK1 |
| C | Hemagglutinin | protein | 315 | 9% helix, 39% strand | Q6VMK1 |
| D | Hemagglutinin | protein | 171 | 55% helix, 12% strand | Q6VMK1 |
| E | Hemagglutinin | protein | 317 | 9% helix, 40% strand | Q6VMK1 |
| F | Hemagglutinin | protein | 169 | 52% helix, 12% strand | Q6VMK1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.84 | 0.97 | 24 | empty |
| 2 | 180 | 0.82 | 0.96 | 26 | empty |
| 3 | 173 | 0.81 | 0.96 | 25 | empty |
| 4 | 177 | 0.81 | 0.96 | 27 | empty |
| 5 | 523 | 0.80 | 0.87 | 40 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3206 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3168 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3102 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 1478 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1456 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4DJ7 · Structure of the hemagglutinin complexed with 3SLN from a highly pathogenic H7N7… · 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 Q6VMK1
- Elsewhere: RCSB PDB 4DJ7 · PDBe 4DJ7 · UniProt Q6VMK1
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