MolNFT v1 · #179702 · protein
SARS-cov-2 D614G 3 rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-D614G)
7KDK · Spike glycoprotein: “SARS-cov-2 D614G 3 rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-D614G)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #179702 on…
- PDB
- 7KDK
- 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, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 972 | 24% helix, 33% 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 | 853 | 0.85 | 0.87 | 122 | empty |
| 2 | 1011 | 0.83 | 0.84 | 104 | empty |
| 3 | 417 | 0.81 | 0.89 | 55 | empty |
| 4 | 741 | 0.80 | 0.84 | 74 | empty |
| 5 | 460 | 0.76 | 0.84 | 50 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5345 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 5310 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 5264 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KDK · SARS-CoV-2 D614G 3 RBD down 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 7KDK · PDBe 7KDK · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.