Research workbench
Potent neutralizing nanobodies resist convergent circulating variants of SARS-cov-2 by targeting novel and conserved epitopes-covs with NB34
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
- 7N9E
- Type
- protein
- Length
- 2,866 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NB34 nanobody; Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | NB34 nanobody | protein | 121 | 5% helix, 38% strand | — |
| A | Spike glycoprotein | protein | 993 | 24% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 809 | 25% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 943 | 23% helix, 30% strand | P0DTC2 |
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 | 967 | 0.86 | 0.87 | 120 | empty |
| 2 | 763 | 0.86 | 0.89 | 109 | empty |
| 3 | 1120 | 0.82 | 0.83 | 108 | empty |
| 4 | 126 | 0.75 | 0.94 | 26 | empty |
| 5 | 402 | 0.75 | 0.85 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4934 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 4065 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 3819 Ų buried · 37 hydrogen bonds · protein-protein
- D–A · 596 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 101 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 35 disulfide (disulfide).
Compared structures
- 7N9E · Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by… · the same entry in another collection · chain D against D, 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 7N9E · PDBe 7N9E · UniProt P0DTC2
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