MolNFT v1 · #186064 · protein
SARS-cov-2 spike with ethylbenzamide-tri-iodo siallyllactose, C3 symmetry
7QUR · Spike GLYCOPROTEIN,FIBRITIN: “SARS-cov-2 spike with ethylbenzamide-tri-iodo siallyllactose, C3 symmetry”. Electron microscopy, 5 ligands (GE9, EIC, NAG), 20 pockets (best druggability 0.86). MolNFT v1 #186064 on GenesisL1: 3D…
- PDB
- 7QUR
- Type
- protein
- Length
- 3,303 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN
- UniProt
- P0DTC2
- Ligands
- GE9, EIC, NAG, FUC, SIA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1101 | 22% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- GE9 · 2,3,5-tris(iodanyl)benzamide · ligand · 3 copies · chains A, B, C
- EIC · Linoleic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, C, B
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains C, A, 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 | 1113 | 0.86 | 0.87 | 128 | empty |
| 2 | 666 | 0.84 | 0.89 | 63 | empty |
| 3 | 211 | 0.84 | 0.97 | 33 | EIC |
| 4 | 1045 | 0.84 | 0.85 | 106 | empty |
| 5 | 222 | 0.84 | 0.96 | 37 | EIC |
Interfaces
3 interfaces between chains.
- A–B · 6678 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 6582 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 6547 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QUR · SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry · 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 P0DTC2
- Elsewhere: RCSB PDB 7QUR · PDBe 7QUR · UniProt P0DTC2
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