MolNFT v1 · #187639 · protein
SARS-cov-2 S B.1.617.1 kappa variant + S309 + S2L20 global refinement
7SOB · Spike glycoprotein: “SARS-cov-2 S B.1.617.1 kappa variant + S309 + S2L20 global refinement”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #187639 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7SOB
- Type
- protein
- Length
- 4,443 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2L20 Fab light chain; S2L20 Fab heavy chain; S309 Fab heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, K | Spike glycoprotein | protein | 1025 | 22% helix, 36% strand | P0DTC2 |
| B, E, L | S2L20 Fab light chain | protein | 107 | 3% helix, 50% strand | — |
| C, F, M | S2L20 Fab heavy chain | protein | 121 | 5% helix, 47% strand | — |
| G, H, N | S309 Fab heavy chain | protein | 128 | 5% helix, 49% strand | — |
| I, J, O | S309 Fab light chain | protein | 100 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, C, B, D, F, E, K, M, L
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 | 1019 | 0.88 | 0.89 | 120 | empty |
| 2 | 999 | 0.87 | 0.88 | 119 | empty |
| 3 | 911 | 0.81 | 0.83 | 82 | empty |
| 4 | 973 | 0.80 | 0.82 | 135 | empty |
| 5 | 870 | 0.79 | 0.82 | 77 | empty |
Interfaces
24 interfaces between chains.
- A–K · 3884 Ų buried · 35 hydrogen bonds · protein-protein
- D–K · 3882 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 3869 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 816 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 7SOB · SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement · 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 7SOB · PDBe 7SOB · UniProt P0DTC2
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