Research workbench
Crystal structure of C13C9 Fab in complex with SARS-cov-2 S fusion peptide
Analyse Crystal structure of C13C9 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
- 7U0E
- Type
- protein
- Length
- 893 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain Fab C13C9; Light chain Fab C13C9; SARS-cov-2 S fusion peptide
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain Fab C13C9 | protein | 223 | 7% helix, 54% strand | — |
| B, L | Light chain Fab C13C9 | protein | 211 | 6% helix, 50% strand | — |
| C, D | SARS-cov-2 S fusion peptide | protein | 12 | 58% helix, 8% strand | — |
| H | Heavy chain Fab C13C9 | protein | 224 | 7% helix, 56% 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 | 736 | 0.67 | 0.75 | 65 | empty |
| 2 | 749 | 0.66 | 0.75 | 64 | empty |
| 3 | 319 | 0.53 | 0.74 | 44 | empty |
| 4 | 213 | 0.47 | 0.74 | 32 | empty |
| 5 | 159 | 0.42 | 0.74 | 33 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1738 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1711 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 10 hydrogen bonds · protein-protein
- C–L · 449 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 434 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7U0E · Crystal Structure of C13C9 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 7U0E · PDBe 7U0E
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