MolNFT v1 · #134313 · protein
Crystal structure of H6 hemagglutinin G225D mutant from taiwan (2013) H6N1 influenza virus in complex with 6'-sln
5T0B: “Crystal structure of H6 hemagglutinin G225D mutant from taiwan (2013) H6N1 influenza virus in complex with…”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 20 pockets (best druggability 0.87). MolNFT v1 #134313 on GenesisL1: 3D…
- PDB
- 5T0B
- Type
- protein
- Length
- 1,498 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Hemagglutinin HA2 chain
- UniProt
- A0A0J9X268, A0A0J9X267
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 330 | 9% helix, 38% strand | A0A0J9X268 |
| B | Hemagglutinin HA2 chain | protein | 173 | 57% helix, 12% strand | A0A0J9X267 |
| C | Hemagglutinin | protein | 326 | 10% helix, 37% strand | A0A0J9X268 |
| D, F | Hemagglutinin HA2 chain | protein | 172 | 56% helix, 13% strand | A0A0J9X267 |
| E | Hemagglutinin | protein | 325 | 10% helix, 38% strand | A0A0J9X268 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E, F
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.87 | 0.88 | 134 | empty |
| 2 | 136 | 0.81 | 0.98 | 21 | empty |
| 3 | 622 | 0.69 | 0.77 | 65 | empty |
| 4 | 230 | 0.61 | 0.81 | 36 | empty |
| 5 | 351 | 0.61 | 0.77 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2745 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2734 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2686 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 1305 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1285 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5T0B · Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2013) H6N1 influenza… · 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 A0A0J9X268
- Every structure of UniProt A0A0J9X267
- Elsewhere: RCSB PDB 5T0B · PDBe 5T0B · UniProt A0A0J9X268 · UniProt A0A0J9X267
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