Research workbench
Crystal structure of SARS-cov spike receptor-binding domain complexed with neutralizing antibody
Analyse Crystal structure of SARS-cov spike receptor-binding domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DD8
- Type
- protein
- Length
- 624 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG heavy chain; IgG light chain; Spike glycoprotein
- UniProt
- Q6PJF1, Q8N355, P59594
- Ligands
- NAG, PO4
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | IgG heavy chain | protein | 220 | 9% helix, 49% strand | Q6PJF1 |
| L | IgG light chain | protein | 212 | 8% helix, 50% strand | Q8N355 |
| S | Spike glycoprotein | protein | 192 | 15% helix, 30% strand | P59594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains S
- PO4 · Phosphate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.55 | 0.79 | 43 | empty |
| 2 | 149 | 0.53 | 0.81 | 26 | empty |
| 3 | 347 | 0.51 | 0.73 | 47 | empty |
| 4 | 130 | 0.41 | 0.75 | 29 | empty |
| 5 | 95 | 0.38 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1761 Ų buried · 18 hydrogen bonds · protein-protein
- H–S · 549 Ų buried · 9 hydrogen bonds · protein-protein
- L–S · 400 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2DD8 · Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing… · the same entry in another collection · chain H against H, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain S against E, TM-score 0.88
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain S against E, TM-score 0.88
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain S against E, TM-score 0.88
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 Q6PJF1
- Every structure of UniProt Q8N355
- Every structure of UniProt P59594
- Elsewhere: RCSB PDB 2DD8 · PDBe 2DD8 · UniProt Q6PJF1 · UniProt Q8N355 · UniProt P59594
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