Research workbench
SARS-cov-2 D614G 1-rbd up spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-D614G)
Analyse SARS-cov-2 D614G 1-rbd up spike protein trimer without the P986-P987… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDL
- Type
- protein
- Length
- 2,875 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 966 | 25% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 949 | 24% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 960 | 25% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 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 | 1039 | 0.83 | 0.84 | 105 | empty |
| 2 | 1108 | 0.83 | 0.84 | 119 | empty |
| 3 | 468 | 0.82 | 0.90 | 58 | empty |
| 4 | 922 | 0.80 | 0.82 | 84 | empty |
| 5 | 694 | 0.76 | 0.81 | 82 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5131 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 4735 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 4177 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 35 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7KDL · SARS-CoV-2 D614G 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing… · 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 7KDL · PDBe 7KDL · UniProt P0DTC2
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