MolNFT v1 · #184472 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-222 and covox-278 fabs
7OR9 · Spike protein S1: “Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-222…”. X-ray diffraction, 3 ligands (NAG, FUC, CL), 10 pockets (best druggability 0.74). MolNFT v1 #184472 on…
- PDB
- 7OR9
- Type
- protein
- Length
- 1,057 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Covox-222 Fab heavy chain; Covox-222 Fab light chain; Covox-278 Fab…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, CL
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike protein S1 | protein | 195 | 18% helix, 31% strand | P0DTC2 |
| A | Covox-222 Fab heavy chain | protein | 215 | 6% helix, 51% strand | — |
| B | Covox-222 Fab light chain | protein | 213 | 7% helix, 55% strand | — |
| H | Covox-278 Fab heavy chain | protein | 220 | 5% helix, 50% strand | — |
| L | Covox-278 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · 4 copies · chains E, A, B
- GOL · Glycerol · additive · 2 copies · chains E, A, B
- PG4 · Tetraethylene glycol · additive · chains E, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.74 | 0.78 | 61 | PG4 |
| 2 | 490 | 0.58 | 0.73 | 51 | CL |
| 3 | 426 | 0.58 | 0.74 | 44 | empty |
| 4 | 167 | 0.53 | 0.79 | 29 | CL |
| 5 | 187 | 0.49 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1708 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1674 Ų buried · 14 hydrogen bonds · protein-protein
- E–A · 734 Ų buried · 18 hydrogen bonds · protein-protein
- E–L · 496 Ų buried · 11 hydrogen bonds · protein-protein
- E–B · 457 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7OR9 · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · the same entry in another collection · chain E against E, 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 7OR9 · PDBe 7OR9 · UniProt P0DTC2
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