Research workbench
Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing antibody COVA2-39
Analyse Crystal structure of SARS-cov-2 receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JMP
- Type
- protein
- Length
- 594 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; COVA2-39 heavy chain; COVA2-39 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 165 | 15% helix, 30% strand | P0DTC2 |
| H | COVA2-39 heavy chain | protein | 218 | 7% helix, 53% strand | — |
| L | COVA2-39 light chain | protein | 211 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.60 | 0.74 | 60 | empty |
| 2 | 183 | 0.47 | 0.75 | 26 | empty |
| 3 | 55 | 0.33 | 0.76 | 17 | empty |
| 4 | 63 | 0.33 | 0.76 | 20 | empty |
| 5 | 50 | 0.31 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1650 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 638 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 160 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JMP · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 7JMP · PDBe 7JMP · UniProt P0DTC2
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