MolNFT v1 · #180207 · protein
SARS-cov-2 spike in complex with nanobodies E
7KSG · Spike glycoprotein: “SARS-cov-2 spike in complex with nanobodies E”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #180207 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KSG
- Type
- protein
- Length
- 3,558 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody against SARS-cov-2 glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1053 | 20% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1062 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1056 | 21% helix, 31% strand | P0DTC2 |
| D, E, F | Nanobody against SARS-cov-2 glycoprotein | protein | 129 | 0% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 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 | 1080 | 0.88 | 0.89 | 124 | empty |
| 2 | 527 | 0.80 | 0.87 | 72 | empty |
| 3 | 388 | 0.76 | 0.86 | 56 | empty |
| 4 | 613 | 0.73 | 0.81 | 45 | empty |
| 5 | 675 | 0.73 | 0.80 | 49 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4335 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 4244 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 4192 Ų buried · 45 hydrogen bonds · protein-protein
- C–F · 930 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 44 disulfide (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7KSG · SARS-CoV-2 spike in complex with nanobodies E · 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 7KSG · PDBe 7KSG · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.