MolNFT v1 · #185551 · protein
Crystal structure of the N-terminal domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-43
7Q0I · Beta-43 heavy chain: “Crystal structure of the N-terminal domain of SARS-cov-2 beta variant spike glycoprotein in complex with…”. X-ray diffraction, 4 ligands (NAG, FUC, CL), 14 pockets (best druggability 0.78). MolNFT v1 #185551 on…
- PDB
- 7Q0I
- Type
- protein
- Length
- 1,441 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-43 heavy chain; Beta-43 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, CL, PO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Beta-43 heavy chain | protein | 229 | 4% helix, 51% strand | — |
| L, B | Beta-43 Fab light chain | protein | 212 | 8% helix, 48% strand | — |
| D | Spike protein S1 | protein | 280 | 3% helix, 54% strand | P0DTC2 |
| C | Spike protein S1 | protein | 279 | 3% helix, 53% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, D, H, C, L
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains D, H
- CL · Chloride ion · ion · 6 copies · chains H, L, A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains H, L, A, B
- PEG · Di(hydroxyethyl)ether · additive · chains H, L
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.78 | 0.80 | 78 | PG4 |
| 2 | 1015 | 0.78 | 0.80 | 82 | empty |
| 3 | 137 | 0.72 | 0.92 | 33 | CL |
| 4 | 742 | 0.67 | 0.75 | 83 | CL |
| 5 | 66 | 0.64 | 0.93 | 27 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2027 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 2018 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 770 Ų buried · 9 hydrogen bonds · protein-protein
- H–C · 751 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q0I · Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein… · 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 7Q0I · PDBe 7Q0I · UniProt P0DTC2
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