Research workbench
Crystal structure of the T478K mutant receptor binding domain of SARS- cov-2 spike glycoprotein in complex with covox-45 and covox-253 fabs
Analyse Crystal structure of the T478K 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
- 7ORA
- Type
- protein
- Length
- 2,124 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Covox-45 Fab heavy chain; Covox-45 Fab light chain; Covox-253 Fab heavy…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, CL
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, C | Spike protein S1 | protein | 197 | 18% helix, 29% strand | P0DTC2 |
| A, D | Covox-45 Fab heavy chain | protein | 216 | 6% helix, 50% strand | — |
| B, E | Covox-45 Fab light chain | protein | 211 | 6% helix, 50% strand | — |
| F, H | Covox-253 Fab heavy chain | protein | 224 | 8% helix, 49% strand | — |
| G, L | Covox-253 Fab light chain | protein | 214 | 8% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains R, F, C, H
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains F, H
- CL · Chloride ion · ion · 6 copies · chains A, B, F, G, H, L
- GOL · Glycerol · additive · 6 copies · chains R, A, B, F, C, D, E, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.64 | 0.76 | 68 | GOL |
| 2 | 676 | 0.63 | 0.74 | 83 | empty |
| 3 | 497 | 0.61 | 0.75 | 64 | empty |
| 4 | 129 | 0.56 | 0.83 | 23 | empty |
| 5 | 232 | 0.56 | 0.78 | 37 | empty |
Interfaces
15 interfaces between chains.
- F–G · 1918 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1830 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1676 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1640 Ų buried · 11 hydrogen bonds · protein-protein
- R–A · 804 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7ORA · Crystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike… · the same entry in another collection · chain R against R, 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 7ORA · PDBe 7ORA · UniProt P0DTC2
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