MolNFT v1 · #184107 · protein
SARS cov-2 spike protein, bristol uk deletion variant, closed conformation, C1 symmetry
7ODL · Spike glycoprotein: “SARS cov-2 spike protein, bristol uk deletion variant, closed conformation, C1 symmetry”. Electron microscopy, 2 ligands (EIC, NAG), 20 pockets (best druggability 0.87). MolNFT v1 #184107 on GenesisL1: 3D…
- PDB
- 7ODL
- Type
- protein
- Length
- 3,066 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- EIC, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1022 | 22% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, C, 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 | 1030 | 0.87 | 0.89 | 113 | empty |
| 2 | 333 | 0.85 | 0.94 | 35 | EIC |
| 3 | 719 | 0.84 | 0.87 | 88 | empty |
| 4 | 509 | 0.84 | 0.90 | 66 | empty |
| 5 | 1085 | 0.84 | 0.85 | 131 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6181 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 6131 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 6127 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7ODL · SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry · 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 7ODL · PDBe 7ODL · UniProt P0DTC2
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