Research workbench
SARS-cov-spike rbd bound to two neutralising nanobodies.
Analyse SARS-cov-spike rbd bound to two neutralising nanobodies. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B17
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; SARS-cov-2 neutralizing biparatopic nanobody VE,NANOBODY E from lama…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.55
Structure
electron microscopy · 2 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 18% helix, 30% strand | P0DTC2 |
| B | SARS-cov-2 neutralizing biparatopic nanobody VE,NANOBODY E from lama GLAMA,SARS-cov-2 neutralizing biparatopic nanobody ve, nanobody E from lama glama | protein | 250 | 4% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.55 | 0.79 | 25 | empty |
| 2 | 85 | 0.32 | 0.73 | 19 | empty |
| 3 | 50 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1978 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7B17 · SARS-CoV-spike RBD bound to two neutralising nanobodies. · 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 7B17 · PDBe 7B17 · UniProt P0DTC2
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