MolNFT v1 · #114492 · protein
Crystal structure of hemagglutinin of A/TAIWAN/2/2013 (H6N1) in complex with lsta
5BR3 · Hemagglutinin HA1 chain: “Crystal structure of hemagglutinin of A/TAIWAN/2/2013 (H6N1) in complex with lsta”. X-ray diffraction, 6 ligands (NAG, MAN, GAL), 10 pockets (best druggability 0.68). MolNFT v1 #114492 on GenesisL1: 3D…
- PDB
- 5BR3
- Type
- protein
- Length
- 994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- Ligands
- NAG, MAN, GAL, SIA, BMA, FUC
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin HA1 chain | protein | 326 | 8% helix, 39% strand | — |
| B, D | Hemagglutinin HA2 chain | protein | 171 | 56% helix, 13% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, B, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.68 | 0.76 | 51 | empty |
| 2 | 57 | 0.49 | 0.85 | 16 | empty |
| 3 | 54 | 0.45 | 0.83 | 13 | empty |
| 4 | 174 | 0.44 | 0.75 | 23 | empty |
| 5 | 67 | 0.42 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2745 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2736 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 289 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5BR3 · PDBe 5BR3
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