Research workbench
SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies
Analyse SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NLL
- Type
- protein
- Length
- 656 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Severe acute respiratory syndrome coronavirus 2; Vicugna pacos
- Molecule
- Spike protein S1; Nanobody Fu2
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.78
Structure
electron microscopy · resolution 2.89 · 4 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike protein S1 | protein | 196 | 15% helix, 26% strand | P0DTC2 |
| D | Spike protein S1 | protein | 195 | 15% helix, 26% strand | P0DTC2 |
| A | Nanobody Fu2 | protein | 133 | 5% helix, 45% strand | — |
| C | Nanobody Fu2 | protein | 132 | 5% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.78 | 0.81 | 94 | empty |
| 2 | 106 | 0.37 | 0.74 | 24 | empty |
| 3 | 76 | 0.36 | 0.76 | 21 | empty |
| 4 | 79 | 0.36 | 0.76 | 21 | empty |
| 5 | 85 | 0.33 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 772 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 766 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 550 Ų buried · 4 hydrogen bonds · protein-protein
- B–A · 548 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7NLL · SARS-cov-2 spike rbd (dimer) in complex with two FU2 nanobodies · 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 7NLL · PDBe 7NLL · UniProt P0DTC2
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