Research workbench
Structure of SARS-cov-2 spike protein with engineered X3 disulfide (X3(D427C, V987C) and single arg S1/S2 cleavage site), locked-122 conformation
Analyse Structure of SARS-cov-2 spike protein with engineered X3 disulfide (X3(D427C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XU1
- Type
- protein
- Length
- 3,309 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- BLA, EIC, NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1110 | 21% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1107 | 21% helix, 29% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1092 | 21% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 3 copies · chains C, B, A
- EIC · Linoleic acid · ligand · 3 copies · chains C, B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains C, A, 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 | 1042 | 0.85 | 0.86 | 126 | empty |
| 2 | 234 | 0.85 | 0.97 | 32 | EIC |
| 3 | 224 | 0.85 | 0.97 | 33 | EIC |
| 4 | 232 | 0.84 | 0.96 | 34 | EIC |
| 5 | 1094 | 0.84 | 0.85 | 116 | empty |
Interfaces
3 interfaces between chains.
- C–B · 6821 Ų buried · 62 hydrogen bonds · protein-protein
- B–A · 6782 Ų buried · 52 hydrogen bonds · protein-protein
- C–A · 6644 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7XU1 · Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and… · 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 7XU1 · PDBe 7XU1 · UniProt P0DTC2
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