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Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59
Analyse Crystal Structure of COVID-19 virus spike receptor-binding domain complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CM4
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.71
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; IgG heavy chain; IgG light chain
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC, NI
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.71 · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 196 | 17% helix, 29% strand | P0DTC2 |
| H | IgG heavy chain | protein | 225 | 8% helix, 52% strand | — |
| L | IgG light chain | protein | 214 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar
- NI · Nickel (II) ion · metal · 2 copies · chains H, L
- EDO · 1,2-ethanediol · additive · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 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 | 0.57 | 0.74 | 55 | EDO |
| 2 | 143 | 0.48 | 0.78 | 21 | empty |
| 3 | 153 | 0.44 | 0.75 | 29 | empty |
| 4 | 91 | 0.39 | 0.77 | 23 | empty |
| 5 | 55 | 0.28 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1969 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 929 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 131 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7CM4 · Crystal structure of COVID-19 virus spike receptor-binding domain complexed 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 7CM4 · PDBe 7CM4 · UniProt P0DTC2
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