MolNFT v1 · #190031 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 delta variant spike glycoprotein in complex with its receptor human ACE2
7WBQ · Angiotensin-converting enzyme 2: “Crystal structure of the receptor binding domain of SARS-cov-2 delta variant spike glycoprotein in complex…”. X-ray diffraction, 3 ligands (NAG, FUL, ZN), 10 pockets (best druggability 0.75). MolNFT…
- PDB
- 7WBQ
- Type
- protein
- Length
- 1,581 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, FUL, ZN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 62% helix, 5% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 195 | 17% helix, 29% strand | P0DTC2 |
| D | Spike protein S1 | protein | 194 | 14% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.75 | 0.77 | 97 | empty |
| 2 | 834 | 0.70 | 0.76 | 71 | empty |
| 3 | 506 | 0.68 | 0.78 | 47 | empty |
| 4 | 393 | 0.62 | 0.77 | 50 | empty |
| 5 | 314 | 0.61 | 0.79 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 925 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 7WBQ · Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike… · 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 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 A against A, TM-score 1.00
- 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 1.00
- 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 1.00
- 3SCK · 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 0.99
- 3SCK · 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 0.99
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 7WBQ · PDBe 7WBQ · UniProt Q9BYF1 · UniProt P0DTC2
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