MolNFT v1 · #145137 · protein
Crystal structure of the A/SOLOMON ISLANDS/3/2006(H1N1) influenza virus hemagglutinin in complex with small molecule JNJ4796
6CF7: “Crystal structure of the A/SOLOMON ISLANDS/3/2006(H1N1) influenza virus hemagglutinin in complex with small…”. X-ray diffraction, 4 ligands (EZ7, NAG, BMA), 5 pockets (best druggability 0.55). MolNFT v1 #145137 on GenesisL1: 3D…
- PDB
- 6CF7
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A7Y8I1, F2NZB4
- Ligands
- EZ7, NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 9% helix, 41% strand | A7Y8I1 |
| B | Hemagglutinin | protein | 171 | 54% helix, 14% strand | F2NZB4 |
Ligands and binding sites
- EZ7 · N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl) methyl]piperazine-1-carbonyl}pyridin-4-yl)-1,3-benzoxazol-5-yl]acetamide · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.55 | 0.78 | 32 | empty |
| 2 | 99 | 0.34 | 0.73 | 18 | empty |
| 3 | 57 | 0.31 | 0.76 | 16 | empty |
| 4 | 66 | 0.30 | 0.74 | 18 | empty |
| 5 | 52 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2752 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6CF7 · Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in… · 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 A7Y8I1
- Every structure of UniProt F2NZB4
- Elsewhere: RCSB PDB 6CF7 · PDBe 6CF7 · UniProt A7Y8I1 · UniProt F2NZB4
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