Research workbench
Potent neutralizing nanobodies resist convergent circulating variants of SARS-cov-2 by targeting novel and conserved epitopes-covs with NB95
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
- 7N9C
- Type
- protein
- Length
- 3,019 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody NB95
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 980 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 812 | 25% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 975 | 24% helix, 31% strand | P0DTC2 |
| D, E | Nanobody NB95 | protein | 126 | 0% helix, 33% 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 | 1118 | 0.83 | 0.84 | 122 | empty |
| 2 | 1056 | 0.83 | 0.84 | 105 | empty |
| 3 | 405 | 0.82 | 0.90 | 58 | empty |
| 4 | 1059 | 0.79 | 0.81 | 92 | empty |
| 5 | 736 | 0.78 | 0.82 | 62 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4300 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4280 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 3969 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 849 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 647 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide (disulfide).
Compared structures
- 7N9C · 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 7N9C · PDBe 7N9C · UniProt P0DTC2
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