MolNFT v1 · #185365 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-29 and beta-53 fabs
7PS2 · Beta-29 Fab light chain: “Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex…”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 9 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 7PS2
- Type
- protein
- Length
- 1,078 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-29 Fab light chain; Spike protein S1; Beta-29 Fab heavy chain; Beta-53 heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-29 Fab light chain | protein | 221 | 5% helix, 50% strand | — |
| G | Spike protein S1 | protein | 197 | 14% helix, 28% strand | P0DTC2 |
| A | Beta-29 Fab heavy chain | protein | 227 | 8% helix, 49% strand | — |
| H | Beta-53 heavy chain | protein | 219 | 4% helix, 50% strand | — |
| L | Beta-53 Fab light chain | protein | 214 | 4% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains G, H
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains H
- SO4 · Sulfate ion · ion · 14 copies · chains B, G, A, H, L
- GOL · Glycerol · additive · 2 copies · chains B, G
- PEG · Di(hydroxyethyl)ether · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.74 | 0.83 | 59 | empty |
| 2 | 434 | 0.58 | 0.75 | 51 | empty |
| 3 | 399 | 0.57 | 0.74 | 51 | empty |
| 4 | 205 | 0.52 | 0.77 | 32 | empty |
| 5 | 185 | 0.48 | 0.76 | 33 | empty |
Interfaces
6 interfaces between chains.
- B–A · 2011 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1854 Ų buried · 14 hydrogen bonds · protein-protein
- G–A · 810 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 620 Ų buried · 10 hydrogen bonds · protein-protein
- G–L · 468 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7PS2 · Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike… · the same entry in another collection · chain B against B, 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 7PS2 · PDBe 7PS2 · UniProt P0DTC2
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