MolNFT v1 · #168339 · protein
Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with small molecule F0045(S)
6WCR: “Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with small…”. X-ray diffraction, 3 ligands (TU7, NAG, BMA), 4 pockets (best druggability 0.56). MolNFT v1 #168339 on GenesisL1: 3D…
- PDB
- 6WCR
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- P03452
- Ligands
- TU7, NAG, BMA
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 8% helix, 42% strand | P03452 |
| B | Hemagglutinin | protein | 171 | 56% helix, 15% strand | P03452 |
Ligands and binding sites
- TU7 · (2,4-dichlorophenyl)[(2S)-2-phenylmorpholin-4-yl]methanone · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.56 | 0.88 | 19 | empty |
| 2 | 166 | 0.45 | 0.75 | 20 | empty |
| 3 | 63 | 0.34 | 0.77 | 17 | empty |
| 4 | 69 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2787 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6WCR · Crystal structure of the A/Puerto Rico/8/1934 (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 P03452
- Elsewhere: RCSB PDB 6WCR · PDBe 6WCR · UniProt P03452
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