MolNFT v1 · #156410 · protein
Cryo-EM structure of sads-cov spike
6M39 · Spike glycoprotein: “Cryo-EM structure of sads-cov spike”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #156410 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6M39
- Type
- protein
- Length
- 2,811 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- A0A2P1G7F5
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 19% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 937 | 19% helix, 26% strand | A0A2P1G7F5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 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 | 931 | 0.88 | 0.90 | 122 | empty |
| 2 | 1138 | 0.87 | 0.88 | 143 | empty |
| 3 | 349 | 0.86 | 0.95 | 59 | empty |
| 4 | 1077 | 0.86 | 0.87 | 123 | empty |
| 5 | 654 | 0.83 | 0.88 | 87 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6285 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 6275 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 6267 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 30 disulfide (N-glycosylation, disulfide).
Compared structures
- 6M39 · Cryo-EM structure of SADS-CoV spike · 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 A0A2P1G7F5
- Elsewhere: RCSB PDB 6M39 · PDBe 6M39 · UniProt A0A2P1G7F5
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