Research workbench
Crystal structure of C13B8 Fab in complex with SARS-cov-2 S fusion peptide
Analyse Crystal structure of C13B8 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
- 7U09
- Type
- protein
- Length
- 446 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain Fab C13B8; Light chain Fab C13B8; SARS-cov-2 S fusion peptide
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain Fab C13B8 | protein | 227 | 5% helix, 49% strand | — |
| L | Light chain Fab C13B8 | protein | 208 | 7% helix, 50% strand | — |
| A | SARS-cov-2 S fusion peptide | protein | 11 | 45% helix, 9% 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 | 425 | 0.55 | 0.73 | 59 | empty |
| 2 | 74 | 0.39 | 0.78 | 23 | empty |
| 3 | 60 | 0.30 | 0.75 | 19 | empty |
| 4 | 75 | 0.30 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1792 Ų buried · 15 hydrogen bonds · protein-protein
- L–A · 450 Ų buried · 8 hydrogen bonds · protein-protein
- H–A · 301 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7U09 · Crystal Structure of C13B8 Fab in complex with SARS-CoV-2 S fusion peptide · 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
- Elsewhere: RCSB PDB 7U09 · PDBe 7U09
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