Research workbench
Structure of unbound MERS-cov spike receptor-binding domain (ENGLAND1 strain).
Analyse Structure of unbound MERS-cov spike receptor-binding domain (ENGLAND1 strain). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZPW
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- K9N5Q8
- Ligands
- NAG, PO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, S | Spike glycoprotein | protein | 208 | 13% helix, 37% strand | K9N5Q8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains R, S
- PO4 · Phosphate ion · ion · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.66 | 0.81 | 30 | PO4 |
| 2 | 115 | 0.46 | 0.79 | 18 | empty |
| 3 | 90 | 0.34 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- R–S · 497 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4ZPW · Structure of unbound MERS-CoV spike receptor-binding domain (England1 strain). · the same entry in another collection · chain R against R, 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 K9N5Q8
- Elsewhere: RCSB PDB 4ZPW · PDBe 4ZPW · UniProt K9N5Q8
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