Research workbench
Crystal structure of H5 hemagglutinin mutant Y161A from A/VIET NAM/1203/2004 H5N1 influenza virus in complex with 3'-gcln
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
- 6E7H
- Type
- protein
- Length
- 1,374 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, GAL, NGC
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 312 | 7% helix, 37% strand | Q5EP31 |
| B | Hemagglutinin HA2 chain | protein | 149 | 54% helix, 7% strand | Q6DQ18 |
| C | Hemagglutinin HA1 chain | protein | 310 | 7% helix, 37% strand | Q5EP31 |
| D | Hemagglutinin HA2 chain | protein | 142 | 55% helix, 4% strand | Q6DQ18 |
| E | Hemagglutinin HA1 chain | protein | 308 | 6% helix, 37% strand | Q5EP31 |
| F | Hemagglutinin HA2 chain | protein | 153 | 56% helix, 3% strand | Q6DQ18 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains C
- NGC · N-glycolyl-alpha-neuraminic acid · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.84 | 0.98 | 23 | empty |
| 2 | 251 | 0.81 | 0.94 | 28 | empty |
| 3 | 799 | 0.81 | 0.84 | 81 | empty |
| 4 | 198 | 0.80 | 0.94 | 29 | empty |
| 5 | 210 | 0.80 | 0.94 | 26 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2420 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2390 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2324 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1416 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1403 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6E7H · 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 6E7H · PDBe 6E7H · UniProt Q5EP31 · UniProt Q6DQ18
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