Research workbench
The SARS-cov-2 spike in complex with the 1.10 neutralizing nanobody
Analyse The SARS-cov-2 spike in complex with the 1.10 neutralizing nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R4R
- Type
- protein
- Length
- 3,293 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Camel-derived nanobody 1.10
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1060 | 20% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1054 | 21% helix, 27% strand | P0DTC2 |
| D | Camel-derived nanobody 1.10 | protein | 119 | 5% helix, 56% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 43 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 | 974 | 0.86 | 0.87 | 124 | empty |
| 2 | 853 | 0.85 | 0.87 | 94 | empty |
| 3 | 604 | 0.82 | 0.87 | 79 | empty |
| 4 | 185 | 0.80 | 0.94 | 37 | empty |
| 5 | 250 | 0.79 | 0.92 | 48 | empty |
Interfaces
4 interfaces between chains.
- B–C · 4237 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3796 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3613 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 25 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7R4R · The SARS-CoV-2 spike in complex with the 1.10 neutralizing nanobody · 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 7R4R · PDBe 7R4R · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.