MolNFT v1 · #121141 · protein
Refinement of the influenza virus hemagglutinin by simulated annealing
5HMG · Hemagglutinin HA1 chain: “Refinement of the influenza virus hemagglutinin by simulated annealing”. X-ray diffraction, 3 ligands (NAG, MAN, SIA), 20 pockets (best druggability 0.88). MolNFT v1 #121141 on GenesisL1: 3D structure…
- PDB
- 5HMG
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- P03437
- Ligands
- NAG, MAN, SIA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 328 | 9% helix, 41% strand | P03437 |
| B, D, F | Hemagglutinin HA2 chain | protein | 175 | 53% helix, 13% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, E, C, B, D, F
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains E, A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.88 | 0.89 | 100 | empty |
| 2 | 1118 | 0.87 | 0.88 | 111 | empty |
| 3 | 94 | 0.75 | 0.97 | 23 | empty |
| 4 | 479 | 0.74 | 0.83 | 60 | empty |
| 5 | 84 | 0.72 | 0.95 | 24 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3117 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3114 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3020 Ų buried · 51 hydrogen bonds · protein-protein
- B–F · 1580 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1574 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5HMG · Refinement of the influenza virus hemagglutinin by simulated annealing · 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 P03437
- Elsewhere: RCSB PDB 5HMG · PDBe 5HMG · UniProt P03437
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.