Research workbench
Crystal structure of a H7 influenza virus hemagglutinin complexed with lstb
Analyse Crystal structure of a H7 influenza virus hemagglutinin complexed with lstb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5J
- Type
- protein
- Length
- 1,447 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- B7NY59, B7NYS1
- Ligands
- NAG, SIA, GAL
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 310 | 9% helix, 38% strand | B7NY59 |
| B | Hemagglutinin | protein | 176 | 53% helix, 14% strand | B7NYS1 |
| C, E | Hemagglutinin | protein | 309 | 7% helix, 40% strand | B7NY59 |
| D | Hemagglutinin | protein | 172 | 52% helix, 15% strand | B7NYS1 |
| F | Hemagglutinin | protein | 171 | 54% helix, 15% strand | B7NYS1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E, B, D, F
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.85 | 0.93 | 39 | GOL |
| 2 | 194 | 0.83 | 0.97 | 22 | GOL |
| 3 | 1077 | 0.81 | 0.83 | 133 | empty |
| 4 | 123 | 0.79 | 0.98 | 22 | empty |
| 5 | 125 | 0.79 | 0.97 | 21 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3301 Ų buried · 46 hydrogen bonds · protein-protein
- E–F · 3228 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3205 Ų buried · 44 hydrogen bonds · protein-protein
- B–F · 1610 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1522 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3M5J · Crystal structure of a H7 influenza virus hemagglutinin complexed with LSTb · 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 3M5J · PDBe 3M5J · UniProt B7NY59 · UniProt B7NYS1
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