Research workbench
Crystal structure of a trimeric influenza hemagglutinin stem in complex with an broadly neutralizing antibody CR9114
Analyse Crystal structure of a trimeric influenza hemagglutinin stem in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CJQ
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Homo sapiens; synthetic construct
- Molecule
- CR9114 light chain; CR9114 heavy chain; Designed influenza hemagglutinin stem #4900, HA1…
- Pockets
- 10 · best druggability 0.58
Structure
x-ray diffraction · resolution 3.6 · 4 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CR9114 light chain | protein | 211 | 9% helix, 50% strand | — |
| H | CR9114 heavy chain | protein | 217 | 6% helix, 53% strand | — |
| A | Designed influenza hemagglutinin stem #4900, HA1 | protein | 52 | 0% helix, 37% strand | — |
| B | Designed influenza hemagglutinin stem #4900, HA2 | protein | 154 | 55% helix, 11% 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 | 468 | 0.58 | 0.74 | 71 | empty |
| 2 | 275 | 0.54 | 0.76 | 38 | empty |
| 3 | 143 | 0.51 | 0.80 | 23 | empty |
| 4 | 50 | 0.49 | 0.87 | 16 | empty |
| 5 | 60 | 0.43 | 0.82 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1840 Ų buried · 32 hydrogen bonds · protein-protein
- L–H · 1713 Ų buried · 14 hydrogen bonds · protein-protein
- H–B · 568 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 263 Ų buried · 2 hydrogen bonds · protein-protein
- L–B · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5CJQ · Crystal structure of a trimeric influenza hemagglutinin stem in complex with an broadly… · 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
- Elsewhere: RCSB PDB 5CJQ · PDBe 5CJQ
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