MolNFT v1 · #179893 · protein
SARS-cov-2 spike glycoprotein, prefusion with one rbd up conformation
7KJ5: “SARS-cov-2 spike glycoprotein, prefusion with one rbd up conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #179893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KJ5
- Type
- protein
- Length
- 2,909 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 967 | 23% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 981 | 23% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 961 | 24% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, C, B
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 | 1073 | 0.85 | 0.86 | 114 | empty |
| 2 | 877 | 0.84 | 0.86 | 112 | empty |
| 3 | 431 | 0.82 | 0.90 | 59 | empty |
| 4 | 335 | 0.81 | 0.91 | 48 | empty |
| 5 | 123 | 0.76 | 0.95 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5342 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 5056 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 4586 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 glycan, 31 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KJ5 · SARS-CoV-2 Spike Glycoprotein, prefusion with one RBD up conformation · 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 7KJ5 · PDBe 7KJ5 · UniProt P0DTC2
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