Research workbench
Crystal structure of the K417T mutant receptor binding domain of SARS- cov-2 spike glycoprotein in complex with covox-222 and EY6A fabs
Analyse Crystal structure of the K417T mutant receptor binding domain of SARS- cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NX8
- 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, CL
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | EY6A Fab heavy chain | protein | 215 | 3% helix, 51% strand | — |
| L | EY6A Fab light chain | protein | 212 | 1% helix, 49% strand | — |
| E | Spike protein S1 | protein | 194 | 15% helix, 31% strand | P0DTC2 |
| A | Covox-222 Fab heavy chain | protein | 215 | 7% helix, 52% strand | — |
| B | Covox-222 Fab light chain | protein | 213 | 8% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- SO4 · Sulfate ion · ion · 12 copies · chains E, A, B
- CL · Chloride ion · ion · 7 copies · chains A, E, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains E, A, B
- GOL · Glycerol · additive · 3 copies · chains E, A, B
- CIT · Citric acid · additive · chains A
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 | 199 | 0.66 | 0.85 | 33 | GOL |
| 2 | 619 | 0.63 | 0.74 | 54 | CIT, PEG, CL |
| 3 | 293 | 0.58 | 0.78 | 49 | GOL |
| 4 | 314 | 0.54 | 0.75 | 37 | empty |
| 5 | 241 | 0.50 | 0.75 | 33 | GOL |
Interfaces
6 interfaces between chains.
- H–L · 1947 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1634 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 731 Ų buried · 22 hydrogen bonds · protein-protein
- H–E · 635 Ų buried · 9 hydrogen bonds · protein-protein
- E–B · 449 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7NX8 · Crystal structure of the K417T mutant receptor binding domain of SARS-CoV-2 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 7NX8 · PDBe 7NX8 · UniProt P0DTC2
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