Research workbench
Crystal structure of SARS-cov-2 beta rbd complexed with P36-5D2 Fab
Analyse Crystal structure of SARS-cov-2 beta rbd complexed with P36-5D2 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FJC
- Type
- protein
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P36-5D2 heavy chain; P36-5D2 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | P36-5D2 heavy chain | protein | 216 | 4% helix, 48% strand | — |
| L | P36-5D2 light chain | protein | 214 | 6% helix, 49% strand | — |
| E | Spike protein S1 | protein | 174 | 16% helix, 27% strand | P0DTC2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.70 | 0.92 | 34 | empty |
| 2 | 267 | 0.67 | 0.83 | 48 | empty |
| 3 | 359 | 0.57 | 0.75 | 56 | empty |
| 4 | 57 | 0.46 | 0.84 | 23 | empty |
| 5 | 132 | 0.38 | 0.73 | 28 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1775 Ų buried · 21 hydrogen bonds · protein-protein
- H–E · 519 Ų buried · 6 hydrogen bonds · protein-protein
- L–E · 386 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7FJC · Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab · 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 7FJC · PDBe 7FJC · UniProt P0DTC2
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