Research workbench
SARS-cov-2 receptor binding domain bound to Fab pdi 42
Analyse SARS-cov-2 receptor binding domain bound to Fab pdi 42 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZG
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pdi 42 heavy chain; Pdi 42 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Pdi 42 heavy chain | protein | 218 | 8% helix, 51% strand | — |
| L | Pdi 42 light chain | protein | 215 | 6% helix, 50% strand | — |
| A | Spike protein S1 | protein | 194 | 19% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- GOL · Glycerol · additive · 6 copies · chains H, A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.62 | 0.88 | 25 | empty |
| 2 | 275 | 0.56 | 0.77 | 39 | empty |
| 3 | 307 | 0.51 | 0.73 | 42 | empty |
| 4 | 52 | 0.33 | 0.78 | 15 | GOL |
| 5 | 52 | 0.23 | 0.71 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1854 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 779 Ų buried · 17 hydrogen bonds · protein-protein
- L–A · 440 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZG · SARS-CoV-2 receptor binding domain bound to Fab PDI 42 · the same entry in another collection · chain H against H, 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 7MZG · PDBe 7MZG · UniProt P0DTC2
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