MolNFT v1 · #179698 · protein
SARS-cov-2 rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas)
7KDG · Spike glycoprotein: “SARS-cov-2 rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #179698 on GenesisL1: 3D…
- PDB
- 7KDG
- Type
- protein
- Length
- 2,916 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 0.85
Structure
electron microscopy · 1 distinct chain · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 972 | 24% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 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 | 862 | 0.85 | 0.87 | 107 | empty |
| 2 | 1132 | 0.83 | 0.84 | 120 | empty |
| 3 | 717 | 0.81 | 0.85 | 77 | empty |
| 4 | 567 | 0.81 | 0.87 | 72 | empty |
| 5 | 335 | 0.77 | 0.88 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5503 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 5453 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 5417 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KDG · SARS-CoV-2 RBD down 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 7KDG · PDBe 7KDG · UniProt P0DTC2
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