MolNFT v1 · #152300 · protein
Crystal structure of H7 hemagglutinin mutant SH1-avpl ( S138A, G186V, T221P, Q226L) from the influenza virus A/SHANGHAI/1/2013 (H7N9)
6IDD: “Crystal structure of H7 hemagglutinin mutant SH1-avpl ( S138A, G186V, T221P, Q226L) from the influenza virus…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #152300 on GenesisL1: 3D structure…
- PDB
- 6IDD
- Type
- protein
- Length
- 2,905 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A0A088BEK2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 485 | 23% helix, 29% strand | A0A088BEK2 |
| C, E, G, I, K | Hemagglutinin | protein | 484 | 25% helix, 28% strand | A0A088BEK2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.83 | 0.97 | 25 | empty |
| 2 | 169 | 0.83 | 0.97 | 20 | empty |
| 3 | 985 | 0.82 | 0.83 | 123 | empty |
| 4 | 172 | 0.82 | 0.97 | 26 | empty |
| 5 | 625 | 0.81 | 0.86 | 45 | empty |
Interfaces
9 interfaces between chains.
- A–G · 2249 Ų buried · 17 hydrogen bonds · protein-protein
- I–K · 2247 Ų buried · 16 hydrogen bonds · protein-protein
- C–K · 2233 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2228 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 2218 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6IDD · Crystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G186V, T221P, Q226L) from… · 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 A0A088BEK2
- Elsewhere: RCSB PDB 6IDD · PDBe 6IDD · UniProt A0A088BEK2
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