MolNFT v1 · #185364 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-27 Fab
7PS1 · Spike protein S1: “Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex…”. X-ray diffraction, 3 ligands (NAG, CL, IOD), 5 pockets (best druggability 0.67). MolNFT v1 #185364 on…
- PDB
- 7PS1
- Type
- protein
- Length
- 622 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Beta-27 Fab heavy chain; Beta-27 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, CL, IOD
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 194 | 15% helix, 31% strand | P0DTC2 |
| A | Beta-27 Fab heavy chain | protein | 215 | 9% helix, 51% strand | — |
| B | Beta-27 Fab light chain | protein | 213 | 8% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- CL · Chloride ion · ion · 4 copies · chains E, A, B
- IOD · Iodide ion · ion · 4 copies · chains E, A, B
- GOL · Glycerol · additive · 4 copies · chains E, A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, E
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 | 328 | 0.67 | 0.81 | 50 | PEG |
| 2 | 355 | 0.54 | 0.74 | 44 | PEG, IOD |
| 3 | 212 | 0.51 | 0.76 | 34 | CL |
| 4 | 133 | 0.38 | 0.73 | 22 | GOL |
| 5 | 52 | 0.25 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1751 Ų buried · 13 hydrogen bonds · protein-protein
- E–A · 791 Ų buried · 19 hydrogen bonds · protein-protein
- E–B · 294 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7PS1 · 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 7PS1 · PDBe 7PS1 · UniProt P0DTC2
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