Research workbench
Crystal structure of SARS-cov-2 rbd Q498Y complexed with human ACE2
Analyse Crystal structure of SARS-cov-2 rbd Q498Y complexed with human ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P19
- Type
- protein
- Length
- 1,549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike protein S1
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN, CL
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 597 | 62% helix, 4% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 176 | 14% helix, 27% strand | P0DTC2 |
| B | Processed angiotensin-converting enzyme 2 | protein | 594 | 61% helix, 4% strand | Q9BYF1 |
| C | Spike protein S1 | protein | 182 | 16% helix, 26% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, E, B, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains E
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.75 | 0.79 | 86 | empty |
| 2 | 988 | 0.73 | 0.76 | 103 | empty |
| 3 | 1151 | 0.72 | 0.76 | 105 | empty |
| 4 | 535 | 0.69 | 0.79 | 49 | empty |
| 5 | 480 | 0.67 | 0.78 | 43 | empty |
Interfaces
4 interfaces between chains.
- B–C · 895 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 829 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 1 hydrogen bond · protein-protein
- E–C · 214 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7P19 · Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2 · the same entry in another collection · chain A against A, 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 B 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 B 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 B 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 B 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 B 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 B against A, TM-score 0.99
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 7P19 · PDBe 7P19 · UniProt Q9BYF1 · UniProt P0DTC2
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