MolNFT v1 · #187221 · protein
Crystal structure of SARS-cov-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody CS23
7S5P · Spike protein S1: “Crystal structure of SARS-cov-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody…”. X-ray diffraction, 2 ligands (NAG, SO4), 6 pockets (best druggability 0.65). MolNFT v1 #187221 on…
- PDB
- 7S5P
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CS23 heavy chain; CS23 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 18% helix, 29% strand | P0DTC2 |
| H | CS23 heavy chain | protein | 212 | 6% helix, 54% strand | — |
| L | CS23 light chain | protein | 210 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 13 copies · chains A, L, H
- EDO · 1,2-ethanediol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.65 | 0.75 | 60 | empty |
| 2 | 129 | 0.57 | 0.84 | 33 | empty |
| 3 | 163 | 0.49 | 0.77 | 24 | empty |
| 4 | 63 | 0.37 | 0.78 | 17 | empty |
| 5 | 79 | 0.31 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1718 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 798 Ų buried · 20 hydrogen bonds · protein-protein
- A–L · 373 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7S5P · Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with… · 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 7S5P · PDBe 7S5P · UniProt P0DTC2
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