MolNFT v1 · #182640 · protein
SARS-cov-2 receptor binding domain bound to Fab pdi 37
7MZF · Spike protein S1: “SARS-cov-2 receptor binding domain bound to Fab pdi 37”. X-ray diffraction, 4 ligands (NAG, FUC, SO4), 5 pockets (best druggability 0.65). MolNFT v1 #182640 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7MZF
- Type
- protein
- Length
- 624 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Pdi 37 heavy chain; Pdi 37 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, SO4, CL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 196 | 18% helix, 30% strand | P0DTC2 |
| H | Pdi 37 heavy chain | protein | 214 | 8% helix, 53% strand | — |
| L | Pdi 37 light chain | protein | 214 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains A, L
- GOL · Glycerol · additive · chains H, 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 | 94 | 0.65 | 0.90 | 22 | CL |
| 2 | 236 | 0.53 | 0.76 | 35 | empty |
| 3 | 168 | 0.51 | 0.78 | 26 | empty |
| 4 | 228 | 0.47 | 0.74 | 37 | empty |
| 5 | 51 | 0.25 | 0.72 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1747 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 808 Ų buried · 21 hydrogen bonds · protein-protein
- A–L · 451 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZF · SARS-CoV-2 receptor binding domain bound to Fab PDI 37 · 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 7MZF · PDBe 7MZF · UniProt P0DTC2
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