Research workbench
MERS-cov S structure in complex with 5-N-acetyl neuraminic acid
Analyse MERS-cov S structure in complex with 5-N-acetyl neuraminic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q04
- Type
- protein
- Length
- 3,477 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- K0BRG7
- Ligands
- FOL, NAG, MAN, BMA, SIA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1159 | 23% helix, 34% strand | K0BRG7 |
Ligands and binding sites
- FOL · Folic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 30 copies · chains C, B, A
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains A, C, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.85 | 0.89 | 83 | empty |
| 2 | 613 | 0.84 | 0.89 | 89 | empty |
| 3 | 808 | 0.84 | 0.86 | 79 | empty |
| 4 | 382 | 0.83 | 0.92 | 65 | empty |
| 5 | 780 | 0.83 | 0.86 | 79 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5901 Ų buried · 78 hydrogen bonds · protein-protein
- A–C · 5897 Ų buried · 77 hydrogen bonds · protein-protein
- B–C · 5887 Ų buried · 77 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q04 · MERS-CoV S structure in complex with 5-N-acetyl neuraminic acid · the same entry in another collection · 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 K0BRG7
- Elsewhere: RCSB PDB 6Q04 · PDBe 6Q04 · UniProt K0BRG7
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