Research workbench
Cryoem structure of SARS-cov-2 rbd in complex with nanobodies NB21 and NB105
Analyse Cryoem structure of SARS-cov-2 rbd in complex with nanobodies NB21 and NB105 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MDW
- Type
- protein
- Length
- 435 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonobody NB21; Spike protein S1; Nanobody NB105
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 6% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonobody NB21 | protein | 117 | 0% helix, 20% strand | — |
| R | Spike protein S1 | protein | 194 | 9% helix, 30% strand | P0DTC2 |
| B | Nanobody NB105 | protein | 124 | 6% helix, 29% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.69 | 0.95 | 20 | empty |
| 2 | 211 | 0.64 | 0.83 | 37 | empty |
| 3 | 74 | 0.64 | 0.92 | 23 | empty |
| 4 | 196 | 0.58 | 0.80 | 38 | empty |
| 5 | 59 | 0.42 | 0.82 | 17 | empty |
Interfaces
2 interfaces between chains.
- R–B · 710 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 630 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MDW · CryoEM structure of SARS-CoV-2 RBD in complex with nanobodies Nb21 and Nb105 · 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 7MDW · PDBe 7MDW · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.