Research workbench
The SARS-cov-2 spike in complex with the 1.29 neutralizing nanobody
Analyse The SARS-cov-2 spike in complex with the 1.29 neutralizing nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R4Q
- Type
- protein
- Length
- 3,414 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Camel-derived nanobody 1.29
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1060 | 20% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1054 | 21% helix, 33% strand | P0DTC2 |
| D, E | Camel-derived nanobody 1.29 | protein | 120 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 43 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 | 972 | 0.88 | 0.89 | 108 | empty |
| 2 | 866 | 0.84 | 0.86 | 95 | empty |
| 3 | 1160 | 0.79 | 0.80 | 97 | empty |
| 4 | 323 | 0.75 | 0.87 | 42 | empty |
| 5 | 229 | 0.75 | 0.90 | 35 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4321 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 3968 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3959 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 770 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 40 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 7R4Q · The SARS-CoV-2 spike in complex with the 1.29 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 7R4Q · PDBe 7R4Q · UniProt P0DTC2
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