Research workbench
SARS-CoV-2 receptor binding domain bound to Fab PDI 210
Analyse SARS-CoV-2 receptor binding domain bound to Fab PDI 210 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZL
- Type
- protein
- Length
- 623 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike protein S1; PDI 210 heavy chain; PDI 210 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · resolution 3.7 · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 16% helix, 30% strand | P0DTC2 |
| H | PDI 210 heavy chain | protein | 216 | 5% helix, 53% strand | — |
| L | PDI 210 light chain | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.54 | 0.77 | 27 | empty |
| 2 | 128 | 0.37 | 0.73 | 28 | empty |
| 3 | 55 | 0.35 | 0.78 | 13 | empty |
| 4 | 80 | 0.31 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1744 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 898 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 273 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZL · SARS-cov-2 receptor binding domain bound to Fab pdi 210 · 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 7MZL · PDBe 7MZL · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.