Research workbench
Structure of SARS-cov-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39
Analyse Structure of SARS-cov-2 spike receptor-binding domain complexed with high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DMU
- Type
- protein
- Length
- 1,586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, MAN, BMA, ZN, SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 64% helix, 4% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 196 | 18% helix, 30% strand | P0DTC2 |
| C | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 598 | 64% helix, 4% strand | Q9BYF1 |
| D | Spike protein S1 | protein | 195 | 14% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies
- BMA · beta-D-mannopyranose · sugar · 5 copies
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.85 | 0.88 | 82 | SO4 |
| 2 | 676 | 0.85 | 0.89 | 93 | SO4 |
| 3 | 147 | 0.67 | 0.87 | 25 | empty |
| 4 | 138 | 0.64 | 0.87 | 23 | empty |
| 5 | 248 | 0.59 | 0.79 | 42 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1002 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 956 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 856 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7DMU · Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.95
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.89
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.89
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.88
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.88
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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7DMU · PDBe 7DMU · UniProt Q9BYF1 · UniProt P0DTC2
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