Research workbench
Structure of SARS-cov-2 D614G spike protein with engineered X3 disulfide (X3(D427C, V987C) and single arg S1/S2 cleavage site), closed conformation
Analyse Structure of SARS-cov-2 D614G spike protein with engineered X3 disulfide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XU5
- Type
- protein
- Length
- 2,814 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- BLA, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 938 | 24% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 3 copies · chains B, A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains B, A, 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 | 1158 | 0.87 | 0.88 | 119 | empty |
| 2 | 630 | 0.81 | 0.86 | 66 | empty |
| 3 | 1042 | 0.81 | 0.82 | 98 | empty |
| 4 | 728 | 0.81 | 0.85 | 78 | empty |
| 5 | 732 | 0.79 | 0.83 | 80 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4834 Ų buried · 41 hydrogen bonds · protein-protein
- B–A · 4833 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 4823 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 36 glycan, 3 cofactor (disulfide, N-glycosylation, biliverdin attachment).
Compared structures
- 7XU5 · Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C… · 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 7XU5 · PDBe 7XU5 · UniProt P0DTC2
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