MolNFT v1 · #185549 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-49 and fi-3A fabs
7Q0G · Spike protein S1: “Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex…”. X-ray diffraction, 6 ligands (NAG, BMA, MAN), 11 pockets (best druggability 0.75). MolNFT v1 #185549 on…
- PDB
- 7Q0G
- Type
- protein
- Length
- 1,063 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Fi-3A Fab heavy chain; Fi-3A Fab light chain; Beta-49 Fab light chain…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN, FUC, K, CL
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 196 | 18% helix, 30% strand | P0DTC2 |
| H | Fi-3A Fab heavy chain | protein | 218 | 7% helix, 50% strand | — |
| L | Fi-3A Fab light chain | protein | 214 | 5% helix, 51% strand | — |
| B | Beta-49 Fab light chain | protein | 216 | 6% helix, 53% strand | — |
| A | Beta-49 Fab heavy chain | protein | 219 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, B, A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains E
- FUC · alpha-L-fucopyranose · sugar · chains E, A
- K · Potassium ion · metal · 14 copies · chains E, H, L, B, A
- CL · Chloride ion · ion · 14 copies · chains E, H, L, B, A
- GOL · Glycerol · additive · 13 copies · chains E, A, H, L, B
- TAR · D(-)-tartaric acid · additive · 3 copies · chains H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.75 | 0.84 | 54 | GOL |
| 2 | 480 | 0.60 | 0.74 | 51 | GOL, K |
| 3 | 382 | 0.56 | 0.74 | 35 | TAR |
| 4 | 303 | 0.55 | 0.75 | 41 | NAG, FUC, GOL, CL |
| 5 | 211 | 0.49 | 0.75 | 31 | K |
Interfaces
6 interfaces between chains.
- B–A · 1882 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1771 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 725 Ų buried · 20 hydrogen bonds · protein-protein
- E–A · 640 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 307 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q0G · Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike… · the same entry in another collection · chain E against E, 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 7Q0G · PDBe 7Q0G · UniProt P0DTC2
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