MolNFT v1 · #139837 · protein
Crystal structure of A/MINNESOTA/11/2010 (H3N2) influenza virus hemagglutinin
5XRT: “Crystal structure of A/MINNESOTA/11/2010 (H3N2) influenza virus hemagglutinin”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #139837 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XRT
- Type
- protein
- Length
- 1,972 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- I0AXC3, R9XUW5
- Ligands
- NAG, MAN, BMA, FUC, FUL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemagglutinin | protein | 319 | 10% helix, 40% strand | I0AXC3 |
| B, D, F, H | Hemagglutinin | protein | 174 | 51% helix, 13% strand | R9XUW5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains A, B, E, C, D, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 32 copies · chains E, C, A
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains E, G
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, E
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.86 | 0.95 | 33 | empty |
| 2 | 445 | 0.85 | 0.92 | 32 | CAC |
| 3 | 900 | 0.82 | 0.84 | 107 | empty |
| 4 | 346 | 0.76 | 0.86 | 30 | empty |
| 5 | 247 | 0.76 | 0.89 | 31 | empty |
Interfaces
17 interfaces between chains.
- A–B · 3171 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 3107 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 3096 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3019 Ų buried · 39 hydrogen bonds · protein-protein
- B–F · 1601 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 glycan, 23 disulfide (N-glycosylation, disulfide).
Compared structures
- 5XRT · Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin · the same entry in another collection · chain E against E, 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
- Every structure of UniProt R9XUW5
- Elsewhere: RCSB PDB 5XRT · PDBe 5XRT · UniProt I0AXC3 · UniProt R9XUW5
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