MolNFT v1 · #97919 · protein
Structure of A/HUBEI/1/2010 H5 ha
4KTH · Hemagglutinin: “Structure of A/HUBEI/1/2010 H5 ha”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #97919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KTH
- Type
- protein
- Length
- 1,462 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- G2U0T8
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 8% helix, 40% strand | G2U0T8 |
| E, C | Hemagglutinin | protein | 321 | 7% helix, 40% strand | G2U0T8 |
| B | Hemagglutinin | protein | 165 | 58% helix, 15% strand | G2U0T8 |
| F | Hemagglutinin | protein | 163 | 55% helix, 15% strand | G2U0T8 |
| D | Hemagglutinin | protein | 170 | 54% helix, 14% strand | G2U0T8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, E, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.83 | 0.84 | 104 | empty |
| 2 | 144 | 0.83 | 0.99 | 18 | empty |
| 3 | 198 | 0.81 | 0.95 | 26 | empty |
| 4 | 193 | 0.81 | 0.95 | 26 | empty |
| 5 | 823 | 0.81 | 0.84 | 62 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2738 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2730 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2728 Ų buried · 38 hydrogen bonds · protein-protein
- F–D · 1668 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1629 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4KTH · Structure of A/Hubei/1/2010 H5 HA · 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 G2U0T8
- Elsewhere: RCSB PDB 4KTH · PDBe 4KTH · UniProt G2U0T8
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