Research workbench
SARS-cov-2 receptor binding domain bound to Fab wcsl 129 and Fab pdi 93
Analyse SARS-cov-2 receptor binding domain bound to Fab wcsl 129 and Fab pdi 93 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZJ
- Type
- protein
- Length
- 2,112 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wcsl 129 light chain; Wcsl 129 heavy chain; Spike protein S1; Pdi 93 light chain; Pdi 93…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | Wcsl 129 light chain | protein | 212 | 8% helix, 49% strand | — |
| C | Wcsl 129 heavy chain | protein | 213 | 4% helix, 52% strand | — |
| B | Spike protein S1 | protein | 198 | 18% helix, 29% strand | P0DTC2 |
| F | Wcsl 129 heavy chain | protein | 214 | 4% helix, 54% strand | — |
| A | Spike protein S1 | protein | 196 | 14% helix, 30% strand | P0DTC2 |
| L | Pdi 93 light chain | protein | 213 | 5% helix, 52% strand | — |
| H | Pdi 93 heavy chain | protein | 222 | 9% helix, 52% strand | — |
| N | Pdi 93 heavy chain | protein | 220 | 9% helix, 53% strand | — |
| M | Pdi 93 light chain | protein | 212 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GOL · Glycerol · additive · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.71 | 0.78 | 80 | empty |
| 2 | 768 | 0.71 | 0.77 | 75 | empty |
| 3 | 515 | 0.69 | 0.79 | 59 | GOL |
| 4 | 550 | 0.62 | 0.75 | 62 | empty |
| 5 | 274 | 0.61 | 0.80 | 51 | empty |
Interfaces
17 interfaces between chains.
- L–H · 1702 Ų buried · 17 hydrogen bonds · protein-protein
- N–M · 1643 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1569 Ų buried · 14 hydrogen bonds · protein-protein
- D–C · 1498 Ų buried · 12 hydrogen bonds · protein-protein
- D–B · 731 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7MZJ · SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 93 · the same entry in another collection · chain N against N, 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 7MZJ · PDBe 7MZJ · UniProt P0DTC2
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