Research workbench
SARS spike glycoprotein - human ACE2 complex, stabilized variant, all ACE2-bound particles
Analyse SARS spike glycoprotein - human ACE2 complex, stabilized variant, all… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CS2
- Type
- protein
- Length
- 3,404 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23
- UniProt
- P59594, D9IEJ2, Q9BYF1
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 891 | 22% helix, 33% strand | P59594, D9IEJ2 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1076 | 21% helix, 33% strand | P59594, D9IEJ2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 893 | 22% helix, 32% strand | P59594, D9IEJ2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 544 | 60% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 20 copies
- MAN · alpha-D-mannopyranose · sugar · 11 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.88 | 0.90 | 132 | empty |
| 2 | 846 | 0.88 | 0.90 | 90 | empty |
| 3 | 910 | 0.78 | 0.80 | 91 | empty |
| 4 | 871 | 0.77 | 0.80 | 99 | empty |
| 5 | 239 | 0.75 | 0.89 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4403 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4354 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4318 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1008 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 33 glycan (disulfide, N-glycosylation).
Compared structures
- 6CS2 · SARS Spike Glycoprotein - human ACE2 complex, Stabilized variant, all ACE2-bound particles · the same entry in another collection · chain C against C, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P59594
- Every structure of UniProt D9IEJ2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 6CS2 · PDBe 6CS2 · UniProt P59594 · UniProt D9IEJ2 · UniProt Q9BYF1
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