MolNFT v1 · #188179 · protein
Cryo-EM structure of SARS-cov-2 kappa (B.1.617.1) spike protein (focused refinement of rbd)
7TF4 · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 kappa (B.1.617.1) spike protein (focused refinement of rbd)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.75). MolNFT v1 #188179 on GenesisL1: 3D…
- PDB
- 7TF4
- Type
- protein
- Length
- 1,608 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Spike glycoprotein | protein | 268 | 10% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.75 | 0.95 | 24 | empty |
| 2 | 83 | 0.73 | 0.96 | 20 | empty |
| 3 | 95 | 0.72 | 0.94 | 23 | empty |
| 4 | 521 | 0.69 | 0.79 | 34 | empty |
| 5 | 428 | 0.62 | 0.76 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–F · 753 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 728 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 695 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 571 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 558 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7TF4 · Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein (focused refinement of… · 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 7TF4 · PDBe 7TF4 · UniProt P0DTC2
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