MolNFT v1 · #180189 · protein
Structural impact on SARS-cov-2 spike protein by D614G substitution
7KRS · Spike glycoprotein: “Structural impact on SARS-cov-2 spike protein by D614G substitution”. Electron microscopy, 3 ligands (NAG, FUC, MAN), 20 pockets (best druggability 0.85). MolNFT v1 #180189 on GenesisL1: 3D structure, binding…
- PDB
- 7KRS
- Type
- protein
- Length
- 3,316 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1109 | 23% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1098 | 23% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1109 | 24% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, C, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
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 | 773 | 0.85 | 0.89 | 103 | empty |
| 2 | 1138 | 0.81 | 0.82 | 109 | empty |
| 3 | 525 | 0.78 | 0.86 | 54 | empty |
| 4 | 331 | 0.76 | 0.88 | 48 | empty |
| 5 | 396 | 0.76 | 0.86 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6484 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 6318 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 5368 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 38 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KRS · Structural impact on SARS-CoV-2 spike protein by D614G substitution · 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 7KRS · PDBe 7KRS · UniProt P0DTC2
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