MolNFT v1 · #186132 · protein
Alpha variant SARS-cov-2 spike in closed conformation
7R13 · Spike glycoprotein: “Alpha variant SARS-cov-2 spike in closed conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #186132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7R13
- Type
- protein
- Length
- 3,003 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1001 | 21% helix, 30% strand | P0DTC2 |
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 | 1175 | 0.85 | 0.86 | 136 | empty |
| 2 | 506 | 0.83 | 0.89 | 62 | empty |
| 3 | 1016 | 0.79 | 0.81 | 95 | empty |
| 4 | 883 | 0.78 | 0.81 | 92 | empty |
| 5 | 908 | 0.78 | 0.81 | 91 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4499 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4497 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4493 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7R13 · Alpha Variant SARS-CoV-2 Spike in Closed conformation · 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 P0DTC2
- Elsewhere: RCSB PDB 7R13 · PDBe 7R13 · UniProt P0DTC2
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