MolNFT v1 · #139836 · protein
Crystal structure of A/MINNESOTA/11/2010 (H3N2) influenza virus hemagglutinin in complex with lstc
5XRS: “Crystal structure of A/MINNESOTA/11/2010 (H3N2) influenza virus hemagglutinin in complex with lstc”. X-ray diffraction, 8 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #139836 on GenesisL1: 3D structure…
- PDB
- 5XRS
- Type
- protein
- Length
- 1,966 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- I0AXC3
- Ligands
- NAG, MAN, BMA, GAL, BGC, SIA, FUL, FUC
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 319 | 10% helix, 37% strand | I0AXC3 |
| B, D, F, H | Hemagglutinin | protein | 172 | 51% helix, 14% strand | I0AXC3 |
| G | Hemagglutinin | protein | 321 | 10% helix, 38% strand | I0AXC3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains A, B, C, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 23 copies · chains C, E, A
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, C, G
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, C, G
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, G
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar
- CAC · Cacodylate ion · additive · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.87 | 0.89 | 117 | CAC |
| 2 | 323 | 0.86 | 0.95 | 35 | empty |
| 3 | 254 | 0.78 | 0.90 | 29 | empty |
| 4 | 298 | 0.76 | 0.88 | 29 | empty |
| 5 | 317 | 0.75 | 0.87 | 29 | empty |
Interfaces
17 interfaces between chains.
- C–D · 3117 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3031 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 3018 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2971 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1513 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 glycan, 23 disulfide (N-glycosylation, disulfide).
Compared structures
- 5XRS · Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin in complex… · 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 I0AXC3
- Elsewhere: RCSB PDB 5XRS · PDBe 5XRS · UniProt I0AXC3
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