MolNFT v1 · #182188 · protein
Cryo-EM structure of the SARS-cov-2 N501Y mutant spike protein ectodomain bound to vh AB8 (focused refinement of rbd and vh AB8)
7MJI · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 N501Y mutant spike protein ectodomain bound to vh AB8 (focused refinement…”. Electron microscopy, 1 ligand (NAG), 1 pocket (best druggability 0.41). MolNFT v1 #182188 on…
- PDB
- 7MJI
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Vh AB8
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.41
Structure
electron microscopy · 2 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike glycoprotein | protein | 195 | 15% helix, 30% strand | P0DTC2 |
| E | Vh AB8 | protein | 125 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.41 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- B–E · 904 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MJI · Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8… · the same entry in another collection · chain B against B, 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 7MJI · PDBe 7MJI · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.