MolNFT v1 · #190715 · protein
Cryo-EM structure of the SARS-cov-2 spike glycoprotein in complex with all-trans retinoic acid
7Y42: “Cryo-EM structure of the SARS-cov-2 spike glycoprotein in complex with all-trans retinoic acid”. Electron microscopy, 2 ligands (REA, NAG), 20 pockets (best druggability 0.86). MolNFT v1 #190715 on GenesisL1: 3D structure, binding…
- PDB
- 7Y42
- Type
- protein
- Length
- 2,904 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- REA, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 21% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Spike glycoprotein | protein | 968 | 21% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- REA · Retinoic acid · ligand · 3 copies · chains A, D, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, D, 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 | 350 | 0.86 | 0.95 | 39 | REA |
| 2 | 742 | 0.86 | 0.89 | 99 | empty |
| 3 | 340 | 0.85 | 0.94 | 41 | REA |
| 4 | 342 | 0.85 | 0.93 | 39 | REA |
| 5 | 787 | 0.80 | 0.83 | 87 | empty |
Interfaces
3 interfaces between chains.
- A–D · 5807 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 5801 Ų buried · 58 hydrogen bonds · protein-protein
- B–D · 5794 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 24 disulfide (N-glycosylation, disulfide).
Compared structures
- 7Y42 · Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic… · the same entry in another collection · chain D against D, 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 7Y42 · PDBe 7Y42 · UniProt P0DTC2
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