Research workbench
SARS-CoV-2 receptor binding domain bound to Fab WCSL 129
Analyse SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZI
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- WCSL 129 light chain; WCSL 129 heavy chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | WCSL 129 light chain | protein | 212 | 8% helix, 47% strand | — |
| H | WCSL 129 heavy chain | protein | 220 | 8% helix, 53% strand | — |
| A | Spike protein S1 | protein | 196 | 18% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 14 copies · chains L, H, A
- PG4 · Tetraethylene glycol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.64 | 0.76 | 56 | GOL |
| 2 | 337 | 0.59 | 0.77 | 49 | GOL |
| 3 | 107 | 0.45 | 0.78 | 16 | empty |
| 4 | 107 | 0.41 | 0.77 | 24 | GOL |
| 5 | 50 | 0.33 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1702 Ų buried · 17 hydrogen bonds · protein-protein
- L–A · 749 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 354 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZI · SARS-cov-2 receptor binding domain bound to Fab wcsl 129 · 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 7MZI · PDBe 7MZI · UniProt P0DTC2
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