Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-269 Fab
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NEH
- Type
- protein
- Length
- 630 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-269 Fab heavy chain; Covox-269 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, NO3, SO4, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Covox-269 Fab heavy chain | protein | 219 | 8% helix, 52% strand | — |
| L | Covox-269 Fab light chain | protein | 215 | 5% helix, 50% strand | — |
| E | Spike glycoprotein | protein | 196 | 17% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
- NO3 · Nitrate ion · ion · 3 copies · chains H, L, E
- SO4 · Sulfate ion · ion · chains L
- CL · Chloride ion · ion · chains H, E
- EDO · 1,2-ethanediol · additive · 19 copies · chains H, E, L
- PEG · Di(hydroxyethyl)ether · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.76 | 0.89 | 30 | EDO, NO3 |
| 2 | 318 | 0.62 | 0.79 | 40 | EDO |
| 3 | 302 | 0.53 | 0.75 | 32 | EDO |
| 4 | 155 | 0.46 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1751 Ų buried · 16 hydrogen bonds · protein-protein
- H–E · 843 Ų buried · 24 hydrogen bonds · protein-protein
- L–E · 517 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent, 1 glycan (disulfide, additive adduct, N-glycosylation).
Compared structures
- 7NEH · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · 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 7NEH · PDBe 7NEH · UniProt P0DTC2
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