MolNFT v1 · #97427 · protein
Crystal structure of the hemagglutinin of A/XINJIANG/1/2006 virus
4KDQ: “Crystal structure of the hemagglutinin of A/XINJIANG/1/2006 virus”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.87). MolNFT v1 #97427 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KDQ
- Type
- protein
- Length
- 1,455 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C5HMM2, Q6J0Q2
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 321 | 9% helix, 41% strand | C5HMM2 |
| B, D, F | Hemagglutinin | protein | 164 | 48% helix, 14% strand | Q6J0Q2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.87 | 0.89 | 132 | empty |
| 2 | 93 | 0.77 | 0.98 | 15 | empty |
| 3 | 792 | 0.68 | 0.75 | 76 | empty |
| 4 | 376 | 0.65 | 0.79 | 47 | empty |
| 5 | 408 | 0.65 | 0.79 | 51 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2577 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2571 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2541 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1456 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1361 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 4KDQ · Crystal structure of the hemagglutinin of A/Xinjiang/1/2006 virus · 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 C5HMM2
- Every structure of UniProt Q6J0Q2
- Elsewhere: RCSB PDB 4KDQ · PDBe 4KDQ · UniProt C5HMM2 · UniProt Q6J0Q2
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