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Crystal structure of H1 hemagglutinin from A/CALIFORNIA/04/2009 in complex with a neutralizing antibody 3E1
Analyse Crystal structure of H1 hemagglutinin from A/CALIFORNIA/04/2009 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GJS
- Type
- protein
- Length
- 905 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Light chain of human neutralizing antibody 3E1; Heavy chain of human…
- UniProt
- C3W5S1
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 320 | 8% helix, 40% strand | C3W5S1 |
| B | Hemagglutinin | protein | 167 | 54% helix, 13% strand | C3W5S1 |
| L | Light chain of human neutralizing antibody 3E1 | protein | 207 | 3% helix, 50% strand | — |
| H | Heavy chain of human neutralizing antibody 3E1 | protein | 211 | 3% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.57 | 0.81 | 25 | empty |
| 2 | 437 | 0.57 | 0.74 | 54 | empty |
| 3 | 260 | 0.48 | 0.73 | 34 | empty |
| 4 | 172 | 0.46 | 0.75 | 20 | empty |
| 5 | 86 | 0.38 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2830 Ų buried · 39 hydrogen bonds · protein-protein
- L–H · 1808 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 540 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 256 Ų buried · 1 hydrogen bond · protein-protein
- A–H · 187 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5GJS · Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a… · 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 C3W5S1
- Elsewhere: RCSB PDB 5GJS · PDBe 5GJS · UniProt C3W5S1
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