Research workbench
SARS-cov-2 receptor binding domain bound to Fab pdi 222
Analyse SARS-cov-2 receptor binding domain bound to Fab pdi 222 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RR0
- Type
- protein
- Length
- 422 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Pdi 222 Fab heavy chain; Pdi 222 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.41
Structure
electron microscopy · 3 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 14% helix, 28% strand | P0DTC2 |
| B | Pdi 222 Fab heavy chain | protein | 121 | 2% helix, 49% strand | — |
| C | Pdi 222 Fab light chain | protein | 107 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.41 | 0.77 | 17 | empty |
| 2 | 117 | 0.37 | 0.74 | 20 | empty |
| 3 | 75 | 0.34 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 844 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 682 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 244 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7RR0 · SARS-CoV-2 receptor binding domain bound to Fab PDI 222 · 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 7RR0 · PDBe 7RR0 · UniProt P0DTC2
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