MolNFT v1 · #96787 · protein
Crystal structure of 2009 pandemic influenza virus hemagglutinin complexed with human receptor analogue lstc
4JTV: “Crystal structure of 2009 pandemic influenza virus hemagglutinin complexed with human receptor analogue lstc”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 20 pockets (best druggability 0.85). MolNFT v1 #96787 on GenesisL1: 3D…
- PDB
- 4JTV
- Type
- protein
- Length
- 2,896 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C3W5S1
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 321 | 9% helix, 36% strand | C3W5S1 |
| B, D, H, J | Hemagglutinin | protein | 162 | 48% helix, 14% strand | C3W5S1 |
| F, L | Hemagglutinin | protein | 161 | 47% helix, 14% strand | C3W5S1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, C, E, I, G
- GAL · beta-D-galactopyranose · sugar · 7 copies · chains A, C, E, I, K
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, C, E, I, K, G
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 | 224 | 0.85 | 0.97 | 26 | empty |
| 2 | 217 | 0.84 | 0.97 | 23 | empty |
| 3 | 1166 | 0.83 | 0.84 | 151 | empty |
| 4 | 1104 | 0.80 | 0.81 | 120 | empty |
| 5 | 108 | 0.78 | 0.97 | 40 | empty |
Interfaces
34 interfaces between chains.
- C–D · 2809 Ų buried · 42 hydrogen bonds · protein-protein
- I–J · 2798 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 2774 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2773 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2759 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4JTV · Crystal structure of 2009 pandemic influenza virus hemagglutinin complexed with human… · the same entry in another collection · chain C against C, 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 4JTV · PDBe 4JTV · UniProt C3W5S1
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