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Crystal structure of SARS-cov-2 fusion peptide in complex with neutralizing antibody COV44-62
Analyse Crystal structure of SARS-cov-2 fusion peptide in complex with neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D36
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutralizing antibody COV44-62 heavy chain; Neutralizing antibody COV44-62 light chain…
- UniProt
- P0DTC2
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Neutralizing antibody COV44-62 heavy chain | protein | 218 | 10% helix, 50% strand | — |
| L | Neutralizing antibody COV44-62 light chain | protein | 212 | 7% helix, 51% strand | — |
| F | Spike protein S2 fusion peptide | protein | 14 | 57% helix, 0% strand | P0DTC2 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.54 | 0.89 | 12 | empty |
| 2 | 307 | 0.53 | 0.74 | 43 | empty |
| 3 | 108 | 0.48 | 0.81 | 23 | empty |
| 4 | 59 | 0.38 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1733 Ų buried · 8 hydrogen bonds · protein-protein
- H–F · 742 Ų buried · 18 hydrogen bonds · protein-protein
- L–F · 191 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 8D36 · Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody… · the same entry in another collection · chain H against H, 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 P0DTC2
- Elsewhere: RCSB PDB 8D36 · PDBe 8D36 · UniProt P0DTC2
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