Research workbench
Crystal structure of CV3-25 Fab bound to SARS-cov-2 spike stem helix peptide
Analyse Crystal structure of CV3-25 Fab bound to SARS-cov-2 spike stem helix peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RAQ
- Type
- protein
- Length
- 455 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CV3-25 Fab heavy chain; CV3-25 Fab light chain; Spike stem helix peptide
- UniProt
- P0DTC2
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CV3-25 Fab heavy chain | protein | 227 | 8% helix, 53% strand | — |
| L | CV3-25 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| P | Spike stem helix peptide | protein | 15 | 33% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, P
- GOL · Glycerol · additive · 7 copies · chains H, L, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.59 | 0.91 | 19 | GOL |
| 2 | 477 | 0.58 | 0.73 | 62 | GOL |
| 3 | 93 | 0.37 | 0.75 | 26 | GOL |
| 4 | 63 | 0.33 | 0.76 | 18 | empty |
| 5 | 68 | 0.29 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2122 Ų buried · 21 hydrogen bonds · protein-protein
- H–P · 643 Ų buried · 17 hydrogen bonds · protein-protein
- L–P · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 7RAQ · Crystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem helix 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
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7RAQ · PDBe 7RAQ · UniProt P0DTC2
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