Research workbench
Crystal structure of a H7 influenza virus hemagglutinin complexed with 6SLN
Analyse Crystal structure of a H7 influenza virus hemagglutinin complexed with 6SLN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5I
- Type
- protein
- Length
- 1,445 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- B7NY59, B7NYS1
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 309 | 8% helix, 38% strand | B7NY59 |
| B | Hemagglutinin | protein | 175 | 53% helix, 15% strand | B7NYS1 |
| D | Hemagglutinin | protein | 172 | 52% helix, 13% strand | B7NYS1 |
| F | Hemagglutinin | protein | 171 | 53% helix, 13% strand | B7NYS1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, E, C, D, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.85 | 0.91 | 43 | empty |
| 2 | 212 | 0.84 | 0.97 | 24 | empty |
| 3 | 978 | 0.83 | 0.84 | 122 | empty |
| 4 | 117 | 0.79 | 0.97 | 21 | empty |
| 5 | 110 | 0.77 | 0.97 | 20 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3271 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 3249 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3206 Ų buried · 46 hydrogen bonds · protein-protein
- B–F · 1663 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1547 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3M5I · Crystal structure of a H7 influenza virus hemagglutinin complexed with 6SLN · 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 B7NY59
- Every structure of UniProt B7NYS1
- Elsewhere: RCSB PDB 3M5I · PDBe 3M5I · UniProt B7NY59 · UniProt B7NYS1
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