Research workbench
Crystal structure of synthetic nanobody (SB14+SB68) complexes with SARS-cov-2 receptor binding domain
Analyse Crystal structure of synthetic nanobody (SB14+SB68) complexes with SARS-cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MFU
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Synthetic nanobody #14 (SB14); Synthetic nanobody #68 (SB68)
- UniProt
- P0DTC2
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Spike protein S1 | protein | 197 | 18% helix, 29% strand | P0DTC2 |
| B, E | Synthetic nanobody #14 (SB14) | protein | 115 | 5% helix, 53% strand | — |
| C, F | Synthetic nanobody #68 (SB68) | protein | 127 | 7% helix, 53% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.75 | 0.78 | 90 | EDO |
| 2 | 602 | 0.72 | 0.80 | 64 | empty |
| 3 | 338 | 0.63 | 0.79 | 37 | empty |
| 4 | 82 | 0.44 | 0.80 | 19 | empty |
| 5 | 61 | 0.41 | 0.81 | 19 | EDO |
Interfaces
8 interfaces between chains.
- D–E · 1170 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1143 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 668 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 430 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7MFU · Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor… · 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 7MFU · PDBe 7MFU · UniProt P0DTC2
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