MolNFT v1 · #101447 · protein
Structure of hemagglutinin with F95Y mutation of influenza virus B/LEE/40
4NRJ · Hemagglutinin HA1 chain: “Structure of hemagglutinin with F95Y mutation of influenza virus B/LEE/40”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.89). MolNFT v1 #101447 on GenesisL1: 3D structure…
- PDB
- 4NRJ
- Type
- protein
- Length
- 1,531 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- P03460
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemagglutinin HA1 chain | protein | 341 | 7% helix, 36% strand | P03460 |
| B | Hemagglutinin HA2 chain | protein | 170 | 52% helix, 12% strand | P03460 |
| C | Hemagglutinin HA1 chain | protein | 342 | 7% helix, 36% strand | P03460 |
| D | Hemagglutinin HA2 chain | protein | 169 | 52% helix, 13% strand | P03460 |
| F | Hemagglutinin HA2 chain | protein | 168 | 52% helix, 13% strand | P03460 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.89 | 0.90 | 139 | empty |
| 2 | 1017 | 0.88 | 0.89 | 92 | empty |
| 3 | 90 | 0.78 | 0.99 | 13 | empty |
| 4 | 181 | 0.72 | 0.89 | 31 | empty |
| 5 | 101 | 0.63 | 0.89 | 33 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2988 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 2940 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2939 Ų buried · 52 hydrogen bonds · protein-protein
- B–F · 1566 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1505 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 4NRJ · Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40 · the same entry in another collection · chain D against D, 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 P03460
- Elsewhere: RCSB PDB 4NRJ · PDBe 4NRJ · UniProt P03460
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