MolNFT v1 · #78556 · protein
Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed with human-civet chimeric receptor ACE2
3SCL · Angiotensin-converting enzyme 2 chimera: “Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed…”. X-ray diffraction, 2 ligands (ZN, CL), 17 pockets (best druggability 0.81).…
- PDB
- 3SCL
- 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 chimera; Spike glycoprotein
- EC
- 3.4.17.23
- UniProt
- Q56NL1, Q9BYF1, P59594
- Ligands
- ZN, CL
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme 2 chimera (EC 3.4.17.23) | protein | 597 | 60% helix, 5% strand | Q56NL1, Q9BYF1 |
| E, F | Spike glycoprotein | protein | 173 | 13% helix, 22% strand | P59594 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.81 | 0.82 | 95 | ZN |
| 2 | 959 | 0.71 | 0.76 | 87 | empty |
| 3 | 52 | 0.62 | 0.93 | 14 | empty |
| 4 | 452 | 0.61 | 0.76 | 48 | empty |
| 5 | 210 | 0.59 | 0.81 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–F · 997 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 997 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 89 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3SCL · Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic… · the same entry in another collection · chain E against E, 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 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 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
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 3SCL · PDBe 3SCL · UniProt Q56NL1 · UniProt Q9BYF1 · UniProt P59594
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