Research workbench
Crystal structure of H5 hemagglutinin mutant Y161A from A/VIET NAM/1203/2004 H5N1 influenza virus
Analyse Crystal structure of H5 hemagglutinin mutant Y161A from A/VIET NAM/1203/2004… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E7G
- Type
- protein
- Length
- 1,422 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q5EP31, Q6DQ18
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 313 | 6% helix, 38% strand | Q5EP31 |
| B | Hemagglutinin HA2 chain | protein | 170 | 54% helix, 13% strand | Q6DQ18 |
| C | Hemagglutinin HA1 chain | protein | 313 | 6% helix, 39% strand | Q5EP31 |
| D | Hemagglutinin HA2 chain | protein | 159 | 55% helix, 6% strand | Q6DQ18 |
| E | Hemagglutinin HA1 chain | protein | 311 | 7% helix, 40% strand | Q5EP31 |
| F | Hemagglutinin HA2 chain | protein | 156 | 53% helix, 3% strand | Q6DQ18 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.84 | 0.98 | 25 | empty |
| 2 | 280 | 0.83 | 0.94 | 29 | empty |
| 3 | 1083 | 0.83 | 0.84 | 86 | empty |
| 4 | 210 | 0.81 | 0.94 | 29 | empty |
| 5 | 282 | 0.78 | 0.90 | 36 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2796 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2534 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2398 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 1546 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1503 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6E7G · Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1… · 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 Q5EP31
- Every structure of UniProt Q6DQ18
- Elsewhere: RCSB PDB 6E7G · PDBe 6E7G · UniProt Q5EP31 · UniProt Q6DQ18
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