MolNFT v1 · #183623 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 B.1.351 variant spike glycoprotein in complex with covox-222 and EY6A fabs
7NXA · EY6A Fab heavy chain: “Crystal structure of the receptor binding domain of SARS-cov-2 B.1.351 variant spike glycoprotein in complex…”. X-ray diffraction, 2 ligands (NAG, SO4), 11 pockets (best druggability 0.63). MolNFT v1 #183623…
- PDB
- 7NXA
- Type
- protein
- Length
- 1,049 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EY6A Fab heavy chain; EY6A Fab light chain; Spike protein S1; Covox-222 Fab heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | EY6A Fab heavy chain | protein | 215 | 3% helix, 49% strand | — |
| L | EY6A Fab light chain | protein | 214 | 6% helix, 52% strand | — |
| E | Spike protein S1 | protein | 193 | 17% helix, 30% strand | P0DTC2 |
| A | Covox-222 Fab heavy chain | protein | 214 | 7% helix, 51% strand | — |
| B | Covox-222 Fab light chain | protein | 213 | 7% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- SO4 · Sulfate ion · ion · 19 copies · chains L, E, A, B
- GOL · Glycerol · additive · 2 copies · chains E, A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.63 | 0.74 | 55 | SO4 |
| 2 | 179 | 0.62 | 0.84 | 31 | SO4 |
| 3 | 508 | 0.59 | 0.74 | 60 | empty |
| 4 | 324 | 0.58 | 0.76 | 47 | GOL |
| 5 | 57 | 0.49 | 0.86 | 22 | GOL, SO4 |
Interfaces
6 interfaces between chains.
- H–L · 1834 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1658 Ų buried · 15 hydrogen bonds · protein-protein
- E–A · 684 Ų buried · 16 hydrogen bonds · protein-protein
- H–E · 659 Ų buried · 10 hydrogen bonds · protein-protein
- E–B · 429 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7NXA · Crystal structure of the receptor binding domain of SARS-CoV-2 B.1.351 variant Spike… · 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 7NXA · PDBe 7NXA · UniProt P0DTC2
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