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Crystal structure of SARS-cov-2 B.1.351 variant receptor binding domain in complex with neutralizing antibodies CS44 and COVA1-16
Analyse Crystal structure of SARS-cov-2 B.1.351 variant receptor binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S5Q
- Type
- protein
- Length
- 1,068 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; CS44 heavy chain; CS44 light chain; COVA1-16 heavy chain; COVA1-16…
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 16 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 198 | 18% helix, 30% strand | P0DTC2 |
| B | CS44 heavy chain | protein | 219 | 3% helix, 53% strand | — |
| C | CS44 light chain | protein | 214 | 7% helix, 51% strand | — |
| H | COVA1-16 heavy chain | protein | 225 | 9% helix, 50% strand | — |
| L | COVA1-16 light chain | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, H, L
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.68 | 0.75 | 72 | empty |
| 2 | 612 | 0.64 | 0.75 | 59 | empty |
| 3 | 606 | 0.62 | 0.74 | 53 | SO4 |
| 4 | 224 | 0.55 | 0.78 | 34 | EDO |
| 5 | 411 | 0.55 | 0.73 | 43 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1727 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1689 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 738 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 526 Ų buried · 8 hydrogen bonds · protein-protein
- B–L · 336 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7S5Q · 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 7S5Q · PDBe 7S5Q · UniProt P0DTC2
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