Research workbench
Cryo-EM structure of SARS-cov-2 spike D614G variant, one rbd-up conformation 2
Analyse Cryo-EM structure of SARS-cov-2 spike D614G variant, one rbd-up conformation 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EB0
- Type
- protein
- Length
- 3,055 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 22% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1013 | 22% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1015 | 21% helix, 25% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1027 | 22% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 77 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 875 | 0.84 | 0.86 | 95 | empty |
| 2 | 1031 | 0.83 | 0.84 | 72 | empty |
| 3 | 556 | 0.82 | 0.87 | 75 | empty |
| 4 | 1169 | 0.80 | 0.82 | 98 | empty |
| 5 | 1097 | 0.79 | 0.81 | 96 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4282 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 4204 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3924 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 35 disulfide (N-glycosylation, disulfide).
Compared structures
- 7EB0 · Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 2 · 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 7EB0 · PDBe 7EB0 · UniProt P0DTC2
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