MolNFT v1 · #165110 · protein
Crystal structure of haemagglutinin from (A/SEAL/GERMANY/1/2014) seal H10N7 influenza virus
6TJY · Hemagglutinin HA1: “Crystal structure of haemagglutinin from (A/SEAL/GERMANY/1/2014) seal H10N7 influenza virus”. X-ray diffraction, 3 ligands (NAG, BMA, CA), 20 pockets (best druggability 0.84). MolNFT v1 #165110 on GenesisL1: 3D…
- PDB
- 6TJY
- Type
- protein
- Length
- 2,949 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- A0A0A7HR51, A0A0A7HNL0
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, I, K | Hemagglutinin HA1 | protein | 320 | 9% helix, 39% strand | A0A0A7HR51 |
| B, D, F, H, J, L | Hemagglutinin HA2 | protein | 172 | 55% helix, 13% strand | A0A0A7HNL0 |
| G | Hemagglutinin HA1 | protein | 317 | 9% helix, 39% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains D, K, C, F, E, A, G, H, L, B, I, J
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 3 copies · chains A, B, H, D, K, L, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.84 | 0.98 | 24 | empty |
| 2 | 191 | 0.84 | 0.98 | 23 | empty |
| 3 | 1199 | 0.84 | 0.85 | 142 | empty |
| 4 | 993 | 0.84 | 0.85 | 118 | empty |
| 5 | 77 | 0.75 | 0.98 | 18 | empty |
Interfaces
30 interfaces between chains.
- C–D · 3349 Ų buried · 40 hydrogen bonds · protein-protein
- K–L · 3345 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 3325 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 3312 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 3311 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6TJY · Crystal structure of haemagglutinin from (A/seal/Germany/1/2014) seal H10N7 influenza… · the same entry in another collection · chain E against E, 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 A0A0A7HR51
- Every structure of UniProt A0A0A7HNL0
- Elsewhere: RCSB PDB 6TJY · PDBe 6TJY · UniProt A0A0A7HR51 · UniProt A0A0A7HNL0
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