Research workbench
Influenza a virus H5 hemagglutinin globular head in complex with antibody AVFLUIGG03
Analyse Influenza a virus H5 hemagglutinin globular head in complex with antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DUP
- Type
- protein
- Length
- 612 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; AVFLUIGG03 heavy chain; AVFLUIGG03 light chain
- UniProt
- Q1WDM0
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 195 | 12% helix, 39% strand | Q1WDM0 |
| H | AVFLUIGG03 heavy chain | protein | 208 | 4% helix, 52% strand | — |
| L | AVFLUIGG03 light chain | protein | 209 | 4% helix, 44% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.59 | 0.74 | 57 | empty |
| 2 | 92 | 0.54 | 0.85 | 23 | empty |
| 3 | 154 | 0.52 | 0.79 | 31 | empty |
| 4 | 201 | 0.48 | 0.76 | 31 | empty |
| 5 | 77 | 0.41 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1740 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 525 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 354 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5DUP · Influenza A virus H5 hemagglutinin globular head in complex with antibody AVFluIgG03 · 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 Q1WDM0
- Elsewhere: RCSB PDB 5DUP · PDBe 5DUP · UniProt Q1WDM0
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