MolNFT v1 · #187385 · protein
Closed state of pre-fusion SARS-cov-2 delta variant spike protein
7SBK · Spike glycoprotein: “Closed state of pre-fusion SARS-cov-2 delta variant spike protein”. Electron microscopy, 3 ligands (NAG, MAN, FUC), 20 pockets (best druggability 0.86). MolNFT v1 #187385 on GenesisL1: 3D structure, binding…
- PDB
- 7SBK
- Type
- protein
- Length
- 3,303 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1101 | 23% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains B, C, A
- MAN · alpha-D-mannopyranose · sugar · 27 copies · chains C, B, A
- FUC · alpha-L-fucopyranose · 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 | 785 | 0.86 | 0.88 | 113 | empty |
| 2 | 506 | 0.83 | 0.89 | 56 | empty |
| 3 | 1160 | 0.81 | 0.83 | 141 | empty |
| 4 | 339 | 0.79 | 0.89 | 55 | empty |
| 5 | 269 | 0.79 | 0.91 | 45 | empty |
Interfaces
3 interfaces between chains.
- B–A · 6160 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 6135 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 6085 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SBK · Closed state of pre-fusion SARS-CoV-2 Delta variant spike protein · the same entry in another collection · chain B against B, 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 7SBK · PDBe 7SBK · UniProt P0DTC2
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