Research workbench
Crystal structure of the L452R mutant receptor binding domain of SARS- cov-2 spike glycoprotein in complex with covox-75 and covox-253 fabs
Analyse Crystal structure of the L452R 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
- 7ORB
- Type
- protein
- Length
- 2,110 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Covox-253 Fab heavy chain; Covox-253 Fab light chain; Covox-75 Fab…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, BMA, MAN, CL, PO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Spike protein S1 | protein | 185 | 16% helix, 26% strand | P0DTC2 |
| H, C | Covox-253 Fab heavy chain | protein | 219 | 11% helix, 51% strand | — |
| L, D | Covox-253 Fab light chain | protein | 214 | 7% helix, 52% strand | — |
| A | Covox-75 Fab heavy chain | protein | 224 | 7% helix, 51% strand | — |
| B, F | Covox-75 Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| X | Spike protein S1 | protein | 184 | 17% helix, 28% strand | P0DTC2 |
| E | Covox-75 Fab heavy chain | protein | 223 | 9% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains R, H, X, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains H, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- CL · Chloride ion · ion · 4 copies · chains H, L, C, D, E, F
- PO4 · Phosphate ion · ion · 3 copies · chains H, A, X, E, C
- GOL · Glycerol · additive · 16 copies · chains R, H, L, A, B, X, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains R, X, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains R, L, X, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.68 | 0.75 | 75 | GOL, PO4 |
| 2 | 586 | 0.67 | 0.77 | 77 | empty |
| 3 | 663 | 0.66 | 0.75 | 65 | PO4 |
| 4 | 431 | 0.63 | 0.78 | 51 | empty |
| 5 | 487 | 0.60 | 0.74 | 62 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1767 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1757 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1747 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1739 Ų buried · 14 hydrogen bonds · protein-protein
- X–C · 605 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7ORB · Crystal structure of the L452R 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 7ORB · PDBe 7ORB · UniProt P0DTC2
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