Research workbench
The receptor binding domain of SARS-cov-2 spike glycoprotein in complex with beta-55 and EY6A fabs
Analyse The receptor binding domain of SARS-cov-2 spike glycoprotein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QNX
- Type
- protein
- Length
- 1,054 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EY6A heavy chain; EY6A light chain; Beta-55 heavy chain; Beta-55 light chain; Surface…
- UniProt
- A0A894R379
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | EY6A heavy chain | protein | 215 | 3% helix, 51% strand | — |
| L | EY6A light chain | protein | 212 | 5% helix, 51% strand | — |
| A | Beta-55 heavy chain | protein | 228 | 8% helix, 52% strand | — |
| B | Beta-55 light chain | protein | 214 | 5% helix, 51% strand | — |
| E | Surface glycoprotein | protein | 185 | 13% helix, 27% strand | A0A894R379 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.65 | 0.74 | 66 | empty |
| 2 | 229 | 0.57 | 0.79 | 38 | empty |
| 3 | 245 | 0.49 | 0.74 | 41 | empty |
| 4 | 153 | 0.47 | 0.76 | 28 | empty |
| 5 | 64 | 0.37 | 0.78 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2093 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1845 Ų buried · 12 hydrogen bonds · protein-protein
- H–E · 688 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 685 Ų buried · 11 hydrogen bonds · protein-protein
- L–E · 468 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7QNX · The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with Beta-55 and… · 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 A0A894R379
- Elsewhere: RCSB PDB 7QNX · PDBe 7QNX · UniProt A0A894R379
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