Research workbench
Cryoem structure of SARS-cov-2 rbd in complex with nanobodies NB21 and NB36
Analyse Cryoem structure of SARS-cov-2 rbd in complex with nanobodies NB21 and NB36 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEJ
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB21; Spike protein S1; Nanobody NB36
- UniProt
- P0DTC2
- Pockets
- 9 · best druggability 0.70
Structure
electron microscopy · 3 distinct chains · 5% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody NB21 | protein | 117 | 0% helix, 21% strand | — |
| R | Spike protein S1 | protein | 194 | 7% helix, 18% strand | P0DTC2 |
| B | Nanobody NB36 | protein | 123 | 5% helix, 5% strand | — |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.70 | 0.87 | 46 | empty |
| 2 | 540 | 0.70 | 0.79 | 64 | empty |
| 3 | 337 | 0.69 | 0.82 | 44 | empty |
| 4 | 79 | 0.62 | 0.89 | 20 | empty |
| 5 | 245 | 0.61 | 0.80 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–R · 576 Ų buried · 1 hydrogen bond · protein-protein
- R–B · 571 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7MEJ · CryoEM structure of SARS-CoV-2 RBD in complex with nanobodies Nb21 and Nb36 · 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 7MEJ · PDBe 7MEJ · UniProt P0DTC2
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