MolNFT v1 · #157580 · protein
Crystal structure of INVBM.18715.A.KN11: influenza hemagglutinin from strain A/NETHERLANDS/002P1/1951
6N41: “Crystal structure of INVBM.18715.A.KN11: influenza hemagglutinin from strain A/NETHERLANDS/002P1/1951”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #157580 on GenesisL1: 3D structure…
- PDB
- 6N41
- Type
- protein
- Length
- 1,448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- E6XTV3
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 483 | 21% helix, 34% strand | E6XTV3 |
| B | Hemagglutinin | protein | 486 | 21% helix, 32% strand | E6XTV3 |
| C | Hemagglutinin | protein | 479 | 23% helix, 33% strand | E6XTV3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.85 | 0.95 | 36 | empty |
| 2 | 812 | 0.81 | 0.84 | 106 | EDO |
| 3 | 133 | 0.78 | 0.96 | 24 | empty |
| 4 | 248 | 0.74 | 0.88 | 36 | EDO |
| 5 | 364 | 0.71 | 0.83 | 54 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2306 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2204 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2148 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 6N41 · Crystal structure of InvbM.18715.a.KN11: Influenza hemagglutinin from strain… · 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 E6XTV3
- Elsewhere: RCSB PDB 6N41 · PDBe 6N41 · UniProt E6XTV3
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