Research workbench
SARS-cov-2 receptor binding domain bound to Fab pdi 231
Analyse SARS-cov-2 receptor binding domain bound to Fab pdi 231 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZN
- Type
- protein
- Length
- 637 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Pdi 231 heavy chain; Pdi 231 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 197 | 15% helix, 29% strand | P0DTC2 |
| H | Pdi 231 heavy chain | protein | 226 | 7% helix, 50% strand | — |
| L | Pdi 231 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.72 | 0.97 | 20 | empty |
| 2 | 236 | 0.53 | 0.77 | 28 | empty |
| 3 | 302 | 0.53 | 0.75 | 44 | empty |
| 4 | 189 | 0.52 | 0.78 | 23 | empty |
| 5 | 80 | 0.42 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1952 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 881 Ų buried · 21 hydrogen bonds · protein-protein
- A–L · 376 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZN · SARS-CoV-2 receptor binding domain bound to Fab PDI 231 · 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 7MZN · PDBe 7MZN · UniProt P0DTC2
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