Research workbench
Crystal structure of VN01H1 Fab in complex with SARS-cov-2 S fusion peptide
Analyse Crystal structure of VN01H1 Fab in complex with SARS-cov-2 S fusion peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SKZ
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-ser-lys-arg-ser-phe-ile-glu-asp-leu-leu-phe-asn; Heavy chain of VN01H1 Fab; Light…
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pro-ser-lys-arg-ser-phe-ile-glu-asp-leu-leu-phe-asn | protein | 12 | 83% helix, 0% strand | — |
| H | Heavy chain of VN01H1 Fab | protein | 226 | 9% helix, 51% strand | — |
| L | Light chain of VN01H1 Fab | protein | 215 | 6% helix, 53% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.59 | 0.74 | 55 | empty |
| 2 | 57 | 0.48 | 0.85 | 21 | empty |
| 3 | 59 | 0.28 | 0.74 | 12 | empty |
| 4 | 54 | 0.24 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2128 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 551 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 124 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7SKZ · Crystal Structure of VN01H1 Fab in complex with SARS-CoV-2 S fusion peptide · 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 7SKZ · PDBe 7SKZ
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