Research workbench
Crystal structure of a H7 influenza virus hemagglutinin
Analyse Crystal structure of a H7 influenza virus hemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M5G
- Type
- protein
- Length
- 1,446 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- B7NY59, B7NYS1
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 310 | 10% helix, 38% strand | B7NY59 |
| B | Hemagglutinin | protein | 174 | 51% helix, 15% strand | B7NYS1 |
| C | Hemagglutinin | protein | 308 | 7% helix, 41% strand | B7NY59 |
| D | Hemagglutinin | protein | 173 | 53% helix, 14% strand | B7NYS1 |
| E | Hemagglutinin | protein | 309 | 8% helix, 40% strand | B7NY59 |
| F | Hemagglutinin | protein | 172 | 52% helix, 13% strand | B7NYS1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, E, C, F, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.87 | 0.88 | 117 | PEG |
| 2 | 164 | 0.82 | 0.97 | 20 | empty |
| 3 | 101 | 0.77 | 0.97 | 20 | empty |
| 4 | 102 | 0.77 | 0.97 | 21 | empty |
| 5 | 1101 | 0.76 | 0.78 | 93 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3310 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 3189 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 3150 Ų buried · 50 hydrogen bonds · protein-protein
- D–F · 1617 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1600 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3M5G · Crystal structure of a H7 influenza virus hemagglutinin · 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 3M5G · PDBe 3M5G · UniProt B7NY59 · UniProt B7NYS1
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