Research workbench
Crystal structure of the haemagglutinin mutant (GLN226LEU, GLY228SER) from an H10N7 seal influenza virus isolated in germany
Analyse Crystal structure of the haemagglutinin mutant (GLN226LEU, GLY228SER) from an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TWH
- Type
- protein
- Length
- 2,943 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Hemagglutinin HA2
- UniProt
- A0A0A7HR51
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 316 | 9% helix, 41% strand | A0A0A7HR51 |
| B, D, F, M, O, Q | Hemagglutinin HA2 | protein | 172 | 54% helix, 15% strand | A0A0A7HR51 |
| C | Hemagglutinin | protein | 315 | 9% helix, 41% strand | A0A0A7HR51 |
| E, P | Hemagglutinin | protein | 322 | 8% helix, 40% strand | A0A0A7HR51 |
| L | Hemagglutinin | protein | 316 | 9% helix, 41% strand | A0A0A7HR51 |
| N | Hemagglutinin | protein | 320 | 8% helix, 41% strand | A0A0A7HR51 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, E, D, C, F, M, P, N, L, O, Q
- CA · Calcium ion · metal · 3 copies · chains B, E, F, N, O, Q, M, P
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 | 1068 | 0.86 | 0.87 | 129 | empty |
| 2 | 200 | 0.84 | 0.97 | 24 | empty |
| 3 | 197 | 0.84 | 0.97 | 23 | empty |
| 4 | 398 | 0.84 | 0.92 | 42 | empty |
| 5 | 107 | 0.78 | 0.97 | 33 | empty |
Interfaces
30 interfaces between chains.
- L–M · 3328 Ų buried · 45 hydrogen bonds · protein-protein
- P–Q · 3318 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3303 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3291 Ų buried · 40 hydrogen bonds · protein-protein
- N–O · 3265 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6TWH · Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal… · 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 A0A0A7HR51
- Elsewhere: RCSB PDB 6TWH · PDBe 6TWH · UniProt A0A0A7HR51
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