Research workbench
Crystal structure of INVBI.18715.A.KN11: influenza hemagglutinin from strain A/JIANGSU/ALSI/2011
Analyse Crystal structure of INVBI.18715.A.KN11: influenza hemagglutinin from strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D8W
- Type
- protein
- Length
- 2,829 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- G0Z9B7
- Ligands
- OXM, NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 466 | 23% helix, 30% strand | G0Z9B7 |
| B | Hemagglutinin | protein | 491 | 23% helix, 31% strand | G0Z9B7 |
| C | Hemagglutinin | protein | 476 | 24% helix, 32% strand | G0Z9B7 |
| D | Hemagglutinin | protein | 443 | 25% helix, 30% strand | G0Z9B7 |
| E | Hemagglutinin | protein | 477 | 22% helix, 31% strand | G0Z9B7 |
| F | Hemagglutinin | protein | 476 | 23% helix, 32% strand | G0Z9B7 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 8 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, E, F
- FMT · Formic acid · additive · chains B
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 | 966 | 0.85 | 0.85 | 92 | empty |
| 2 | 215 | 0.84 | 0.97 | 23 | empty |
| 3 | 423 | 0.77 | 0.86 | 59 | empty |
| 4 | 544 | 0.77 | 0.84 | 61 | empty |
| 5 | 857 | 0.75 | 0.79 | 101 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1749 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1728 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 1720 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1720 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1606 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6D8W · Crystal structure of InvbI.18715.a.KN11: Influenza hemagglutinin from strain… · 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 G0Z9B7
- Elsewhere: RCSB PDB 6D8W · PDBe 6D8W · UniProt G0Z9B7
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