Research workbench
Crystal structure of nanobody NB112 and SARS-cov-2 rbd
Analyse Crystal structure of nanobody NB112 and SARS-cov-2 rbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RBY
- Type
- protein
- Length
- 650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Ilama-isolated nanobody nih-cov nb-112 specific to SARS- cov-2 rbd
- UniProt
- P0DTC2
- Ligands
- NAG, MG
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike protein S1 | protein | 195 | 15% helix, 29% strand | P0DTC2 |
| B, D | Ilama-isolated nanobody nih-cov nb-112 specific to SARS- cov-2 rbd | protein | 130 | 2% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.35 | 0.77 | 18 | empty |
| 2 | 81 | 0.31 | 0.73 | 22 | empty |
| 3 | 61 | 0.30 | 0.75 | 15 | empty |
| 4 | 55 | 0.27 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1146 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1115 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 326 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7RBY · Crystal structure of Nanobody nb112 and SARS-CoV-2 RBD · 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 7RBY · PDBe 7RBY · UniProt P0DTC2
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