MolNFT v1 · #143712 · protein
Cryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state
6B7N: “Cryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.89). MolNFT v1 #143712 on GenesisL1: 3D structure, binding…
- PDB
- 6B7N
- Type
- protein
- Length
- 2,898 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein
- UniProt
- A0A075E3D7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike protein | protein | 966 | 23% helix, 28% strand | A0A075E3D7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 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 | 835 | 0.89 | 0.92 | 110 | empty |
| 2 | 383 | 0.84 | 0.92 | 59 | empty |
| 3 | 352 | 0.82 | 0.92 | 67 | empty |
| 4 | 400 | 0.82 | 0.90 | 70 | empty |
| 5 | 340 | 0.79 | 0.90 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6117 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 6115 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 6035 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 6B7N · Cryo-electron microscopy structure of porcine delta coronavirus spike protein in the… · 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 A0A075E3D7
- Elsewhere: RCSB PDB 6B7N · PDBe 6B7N · UniProt A0A075E3D7
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