MolNFT v1 · #182646 · protein
SARS-cov-2 receptor binding domain bound to Fab pdi 210
7MZL · Spike protein S1: “SARS-cov-2 receptor binding domain bound to Fab pdi 210”. X-ray diffraction, 2 ligands (NAG, FUC), 4 pockets (best druggability 0.54). MolNFT v1 #182646 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7MZL
- Type
- protein
- Length
- 623 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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
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