Research workbench
SARS-cov-2 rbd up spike protein trimer without the P986-P987 stabilizing mutations (S-gsas)
Analyse SARS-cov-2 rbd up spike protein trimer without the P986-P987 stabilizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDH
- Type
- protein
- Length
- 2,891 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 0.84
Structure
electron microscopy · 3 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 970 | 24% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 958 | 24% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 963 | 24% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains A, B, 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 | 699 | 0.84 | 0.88 | 79 | empty |
| 2 | 1181 | 0.83 | 0.84 | 103 | empty |
| 3 | 1154 | 0.83 | 0.84 | 118 | empty |
| 4 | 569 | 0.81 | 0.87 | 66 | empty |
| 5 | 615 | 0.75 | 0.81 | 80 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5265 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 4942 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 4329 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 35 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7KDH · SARS-CoV-2 RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations… · 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 7KDH · PDBe 7KDH · UniProt P0DTC2
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