MolNFT v1 · #169929 · protein
Distinct conformational states of SARS-cov-2 spike protein
6XRA · Spike glycoprotein: “Distinct conformational states of SARS-cov-2 spike protein”. Electron microscopy, 2 ligands (NAG, MAN), 13 pockets (best druggability 0.79). MolNFT v1 #169929 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XRA
- Type
- protein
- Length
- 1,044 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | Spike glycoprotein | protein | 348 | 49% helix, 22% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains C, B, A
- MAN · alpha-D-mannopyranose · sugar · 18 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.79 | 0.82 | 72 | empty |
| 2 | 96 | 0.78 | 0.98 | 15 | empty |
| 3 | 1188 | 0.77 | 0.79 | 89 | empty |
| 4 | 64 | 0.74 | 0.99 | 15 | empty |
| 5 | 114 | 0.42 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6714 Ų buried · 83 hydrogen bonds · protein-protein
- C–A · 6697 Ų buried · 84 hydrogen bonds · protein-protein
- C–B · 6684 Ų buried · 82 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6XRA · Distinct conformational states of SARS-CoV-2 spike protein · the same entry in another collection · chain C against C, 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 6XRA · PDBe 6XRA · UniProt P0DTC2
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