Research workbench
The crystal structure of rbd-nanobody complex, DL28 (SC4)
Analyse The crystal structure of rbd-nanobody complex, DL28 (SC4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F5H
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARS-cov-2 spike receptor-binding domain (rbd); Nanobody DL28
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, FUC, PO4
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARS-cov-2 spike receptor-binding domain (rbd) | protein | 196 | 17% helix, 28% strand | P0DTC2 |
| B | SARS-cov-2 spike receptor-binding domain (rbd) | protein | 196 | 14% helix, 28% strand | P0DTC2 |
| C | Nanobody DL28 | protein | 114 | 5% helix, 54% strand | — |
| D | Nanobody DL28 | protein | 120 | 5% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.53 | 0.80 | 25 | empty |
| 2 | 117 | 0.45 | 0.78 | 24 | empty |
| 3 | 116 | 0.42 | 0.76 | 21 | empty |
| 4 | 110 | 0.41 | 0.77 | 22 | empty |
| 5 | 93 | 0.36 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1104 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1050 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 897 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7F5H · The crystal structure of RBD-Nanobody complex, DL28 (SC4) · 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 7F5H · PDBe 7F5H · UniProt P0DTC2
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