MolNFT v1 · #96789 · protein
Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E
4JTX: “Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #96789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JTX
- Type
- protein
- Length
- 2,908 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C3W5S1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 323 | 8% helix, 39% strand | C3W5S1 |
| B, H | Hemagglutinin | protein | 162 | 48% helix, 15% strand | C3W5S1 |
| C, G, I, K | Hemagglutinin | protein | 322 | 8% helix, 39% strand | C3W5S1 |
| D | Hemagglutinin | protein | 164 | 47% helix, 16% strand | C3W5S1 |
| E | Hemagglutinin | protein | 321 | 8% helix, 40% strand | C3W5S1 |
| F, L | Hemagglutinin | protein | 161 | 48% helix, 16% strand | C3W5S1 |
| J | Hemagglutinin | protein | 166 | 46% helix, 16% strand | C3W5S1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, I, E, G, K
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 | 192 | 0.83 | 0.97 | 23 | empty |
| 2 | 193 | 0.83 | 0.96 | 23 | empty |
| 3 | 1166 | 0.80 | 0.82 | 118 | empty |
| 4 | 535 | 0.79 | 0.85 | 68 | empty |
| 5 | 102 | 0.77 | 0.97 | 32 | empty |
Interfaces
34 interfaces between chains.
- A–B · 2840 Ų buried · 42 hydrogen bonds · protein-protein
- K–L · 2839 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2811 Ų buried · 40 hydrogen bonds · protein-protein
- I–J · 2806 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2805 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4JTX · Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E · 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 C3W5S1
- Elsewhere: RCSB PDB 4JTX · PDBe 4JTX · UniProt C3W5S1
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