Research workbench
Crystal structure of SARS-cov-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79
Analyse Crystal structure of SARS-cov-2 spike stem fusion peptide 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
- 8DAO
- Type
- protein
- Length
- 912 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COV44-79 heavy chain variable domain; COV44-79 light chain variable domain; COV44-79…
- UniProt
- P0DOX5, P01834, P0DTC2
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | COV44-79 heavy chain variable domain | protein | 126 | 7% helix, 46% strand | — |
| D, B | COV44-79 light chain variable domain | protein | 109 | 3% helix, 49% strand | — |
| E, G | COV44-79 heavy chain constant domain | protein | 103 | 6% helix, 50% strand | P0DOX5 |
| F, H | COV44-79 light chain constant domain | protein | 106 | 8% helix, 53% strand | P01834 |
| I, J | Spike protein S2 fusion peptide | protein | 12 | 75% helix, 0% strand | P0DTC2 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.65 | 0.77 | 48 | empty |
| 2 | 449 | 0.62 | 0.76 | 38 | empty |
| 3 | 291 | 0.59 | 0.78 | 35 | empty |
| 4 | 397 | 0.57 | 0.74 | 45 | empty |
| 5 | 341 | 0.55 | 0.75 | 38 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1075 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1069 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1061 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 916 Ų buried · 5 hydrogen bonds · protein-protein
- A–J · 605 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 8DAO · Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing… · the same entry in another collection · chain C against C, 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 P0DOX5
- Every structure of UniProt P01834
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8DAO · PDBe 8DAO · UniProt P0DOX5 · UniProt P01834 · UniProt P0DTC2
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