Research workbench
Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2
Analyse Crystal structure of spike protein receptor-binding domain from the 2002-2003… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D0G
- Type
- protein
- Length
- 1,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike glycoprotein
- EC
- 3.4.17.23
- UniProt
- Q56NL1, Q9BYF1, P59594
- Ligands
- NDG, NAG, ZN, CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 597 | 62% helix, 5% strand | Q56NL1, Q9BYF1 |
| E, F | Spike glycoprotein | protein | 173 | 16% helix, 25% strand | P59594 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 5 copies · chains A, B, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.78 | 0.81 | 66 | ZN |
| 2 | 970 | 0.77 | 0.79 | 105 | empty |
| 3 | 526 | 0.64 | 0.76 | 51 | empty |
| 4 | 437 | 0.63 | 0.77 | 54 | empty |
| 5 | 337 | 0.61 | 0.78 | 37 | empty |
Interfaces
3 interfaces between chains.
- B–F · 995 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 972 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 135 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3D0G · Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS… · the same entry in another collection · chain E against E, 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 0.99
- 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 0.99
- 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
- 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
- 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 0.99
- 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 0.99
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 Q56NL1
- Every structure of UniProt Q9BYF1
- Every structure of UniProt P59594
- Elsewhere: RCSB PDB 3D0G · PDBe 3D0G · UniProt Q56NL1 · UniProt Q9BYF1 · UniProt P59594
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.