Research workbench
SARS-cov-2 beta rbd in complex with nanobody C1, omi-18 and omi-31 fabs
Analyse SARS-cov-2 beta rbd in complex with nanobody C1, omi-18 and omi-31 fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZFC
- Type
- protein
- Length
- 1,180 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omi-31 heavy chain; Omi-31 light chain; Nanobody C1; Omi-18 heavy chain; Omi-18 light…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Omi-31 heavy chain | protein | 228 | 7% helix, 53% strand | — |
| L | Omi-31 light chain | protein | 213 | 7% helix, 49% strand | — |
| M | Nanobody C1 | protein | 124 | 7% helix, 52% strand | — |
| A | Omi-18 heavy chain | protein | 215 | 7% helix, 53% strand | — |
| B | Omi-18 light chain | protein | 207 | 7% helix, 51% strand | — |
| E | Spike protein S1 | protein | 193 | 15% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- FUC · alpha-L-fucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.75 | 0.85 | 49 | empty |
| 2 | 635 | 0.64 | 0.75 | 62 | empty |
| 3 | 337 | 0.61 | 0.78 | 39 | empty |
| 4 | 388 | 0.56 | 0.74 | 53 | empty |
| 5 | 159 | 0.53 | 0.80 | 25 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1896 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1714 Ų buried · 17 hydrogen bonds · protein-protein
- H–E · 939 Ų buried · 10 hydrogen bonds · protein-protein
- M–E · 819 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 745 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZFC · SARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs · the same entry in another collection · chain H against H, 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 7ZFC · PDBe 7ZFC · UniProt P0DTC2
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