Research workbench
Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody
Analyse Structure of COVID-19 virus spike receptor-binding domain complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BZ5
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Heavy chain of B38; Light chain of B38
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 15% helix, 30% strand | P0DTC2 |
| H | Heavy chain of B38 | protein | 218 | 8% helix, 51% strand | — |
| L | Light chain of B38 | protein | 216 | 6% helix, 50% 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.67 | 0.83 | 41 | empty |
| 2 | 278 | 0.61 | 0.79 | 40 | empty |
| 3 | 338 | 0.53 | 0.74 | 47 | empty |
| 4 | 51 | 0.49 | 0.87 | 22 | empty |
| 5 | 82 | 0.32 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1681 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 775 Ų buried · 21 hydrogen bonds · protein-protein
- A–L · 550 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7BZ5 · Structure of COVID-19 virus spike receptor-binding domain complexed with a 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 7BZ5 · PDBe 7BZ5 · UniProt P0DTC2
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