Research workbench
SARS cov-2 spike protein, closed conformation, C1 symmetry
Analyse SARS cov-2 spike protein, closed conformation, C1 symmetry in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZB4
- Type
- protein
- Length
- 3,133 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 · 3 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1035 | 20% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1050 | 20% helix, 27% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1048 | 19% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 3 copies · chains C, B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains C, B, A
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 | 1054 | 0.87 | 0.88 | 126 | empty |
| 2 | 809 | 0.87 | 0.90 | 93 | empty |
| 3 | 347 | 0.85 | 0.94 | 42 | EIC |
| 4 | 338 | 0.85 | 0.94 | 35 | EIC |
| 5 | 330 | 0.84 | 0.93 | 39 | EIC |
Interfaces
3 interfaces between chains.
- C–A · 6192 Ų buried · 33 hydrogen bonds · protein-protein
- B–A · 6150 Ų buried · 39 hydrogen bonds · protein-protein
- C–B · 6057 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZB4 · SARS CoV-2 Spike protein, Closed conformation, C1 symmetry · the same entry in another collection · chain C against C, 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 6ZB4 · PDBe 6ZB4 · UniProt P0DTC2
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