Research workbench
Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab
Analyse Crystal structure of SARS-cov-2 spike protein receptor-binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CWV
- Type
- protein
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Vhh 2-31; CC12.1 Fab heavy chain; CC12.1 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 197 | 12% helix, 30% strand | P0DTC2 |
| B | Vhh 2-31 | protein | 124 | 13% helix, 47% strand | — |
| H | CC12.1 Fab heavy chain | protein | 218 | 8% helix, 52% strand | — |
| L | CC12.1 Fab light chain | protein | 215 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.71 | 0.80 | 51 | empty |
| 2 | 60 | 0.48 | 0.85 | 21 | empty |
| 3 | 229 | 0.47 | 0.73 | 36 | empty |
| 4 | 72 | 0.37 | 0.77 | 13 | empty |
| 5 | 64 | 0.36 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- H–L · 2046 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 764 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 541 Ų buried · 13 hydrogen bonds · protein-protein
- B–L · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 8CWV · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a… · 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
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8CWV · PDBe 8CWV · UniProt P0DTC2
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