Research workbench
Potent neutralizing nanobodies resist convergent circulating variants of SARS-cov-2 by targeting novel and conserved epitopes-covs with NB21
Analyse Potent neutralizing nanobodies resist convergent circulating variants of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N9B
- Type
- protein
- Length
- 3,197 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; NB21 nanobody
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 989 | 22% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 986 | 23% helix, 27% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 988 | 22% helix, 29% strand | P0DTC2 |
| D, F | NB21 nanobody | protein | 117 | 3% helix, 46% strand | — |
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 | 1185 | 0.87 | 0.89 | 137 | empty |
| 2 | 788 | 0.84 | 0.87 | 102 | empty |
| 3 | 1062 | 0.80 | 0.81 | 120 | empty |
| 4 | 1142 | 0.77 | 0.79 | 117 | empty |
| 5 | 749 | 0.77 | 0.82 | 91 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5090 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 4718 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4294 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 819 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 761 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 7N9B · Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by… · 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 7N9B · PDBe 7N9B · UniProt P0DTC2
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