MolNFT v1 · #134524 · protein
Crystal structure of the A/SHANGHAI/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral drug arbidol
5T6S · Hemagglutinin HA1: “Crystal structure of the A/SHANGHAI/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral…”. X-ray diffraction, 4 ligands (75U, NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5T6S
- Type
- protein
- Length
- 2,922 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- R4NN21
- Ligands
- 75U, NAG, BMA, NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin HA1 | protein | 316 | 9% helix, 40% strand | R4NN21 |
| B, D, F, H, J, L | Hemagglutinin HA2 | protein | 171 | 52% helix, 15% strand | R4NN21 |
Ligands and binding sites
- 75U · ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-[(phenylsulfanyl)methyl]-1H-indole-3-carboxylate · ligand · 6 copies · chains A, B, E, F, C, D, G, H, I, J, K, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains C, D, E, F, G, H, I, J, K, L, A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies
- NA · Sodium ion · metal · chains H, J, L
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 | 177 | 0.84 | 0.98 | 22 | empty |
| 2 | 177 | 0.83 | 0.98 | 19 | empty |
| 3 | 571 | 0.82 | 0.88 | 65 | 75U |
| 4 | 567 | 0.82 | 0.87 | 64 | 75U |
| 5 | 309 | 0.82 | 0.92 | 31 | empty |
Interfaces
31 interfaces between chains.
- C–D · 3143 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 3137 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3136 Ų buried · 45 hydrogen bonds · protein-protein
- I–J · 3093 Ų buried · 44 hydrogen bonds · protein-protein
- K–L · 3084 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 5T6S · Crystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus hemagglutinin in… · 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 R4NN21
- Elsewhere: RCSB PDB 5T6S · PDBe 5T6S · UniProt R4NN21
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