MolNFT v1 · #139111 · protein
Prefusion structure of SARS-cov spike glycoprotein, conformation 1
5X58: “Prefusion structure of SARS-cov spike glycoprotein, conformation 1”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #139111 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X58
- Type
- protein
- Length
- 3,159 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1054 | 19% helix, 27% strand | — |
| B | Spike glycoprotein | protein | 1053 | 19% helix, 27% strand | — |
| C | Spike glycoprotein | protein | 1052 | 19% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 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 | 1156 | 0.87 | 0.88 | 151 | empty |
| 2 | 720 | 0.83 | 0.86 | 98 | empty |
| 3 | 1186 | 0.81 | 0.83 | 129 | empty |
| 4 | 625 | 0.81 | 0.86 | 94 | empty |
| 5 | 548 | 0.80 | 0.86 | 81 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5931 Ų buried · 62 hydrogen bonds · protein-protein
- B–C · 5896 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 5887 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 glycan, 18 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5X58 · Prefusion structure of SARS-CoV spike glycoprotein, conformation 1 · 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
- Elsewhere: RCSB PDB 5X58 · PDBe 5X58
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