Research workbench
Crystal structure of SARS-cov-2 spike protein receptor-binding domain in complex with cross-neutralizing antibody COVA1-16 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
- 7JMW
- Type
- protein
- Length
- 638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; COVA1-16 heavy chain; COVA1-16 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 15% helix, 29% strand | P0DTC2 |
| H | COVA1-16 heavy chain | protein | 230 | 4% helix, 50% strand | — |
| L | COVA1-16 light chain | protein | 213 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.64 | 0.74 | 56 | empty |
| 2 | 66 | 0.62 | 0.92 | 21 | empty |
| 3 | 230 | 0.56 | 0.78 | 34 | empty |
| 4 | 193 | 0.45 | 0.74 | 36 | empty |
| 5 | 116 | 0.42 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1743 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 685 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 182 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JMW · Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with… · 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 7JMW · PDBe 7JMW · UniProt P0DTC2
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