Research workbench
SARS-cov-2 spike receptor-binding domain (rbd) in complex with S2E12 Fab, S309 Fab, and S304 Fab
Analyse SARS-cov-2 spike receptor-binding domain (rbd) in complex with S2E12 Fab, S309… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R6X
- Type
- protein
- Length
- 1,189 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody S304 Fab light chain; Monoclonal antibody S304 Fab heavy chain; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG, CL
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Monoclonal antibody S304 Fab light chain | protein | 164 | 4% helix, 48% strand | — |
| H | Monoclonal antibody S304 Fab heavy chain | protein | 186 | 5% helix, 50% strand | — |
| R | Spike protein S1 | protein | 199 | 17% helix, 29% strand | P0DTC2 |
| B | Monoclonal antibody S309 Fab light chain | protein | 213 | 6% helix, 52% strand | — |
| A | Monoclonal antibody S309 Fab heavy chain | protein | 227 | 10% helix, 51% strand | — |
| D | Monoclonal antibody S2E12 Fab light chain | protein | 78 | 4% helix, 46% strand | — |
| C | Monoclonal antibody S2E12 Fab heavy chain | protein | 122 | 10% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains R, B, A
- CL · Chloride ion · ion · 2 copies · chains L, H, R, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.61 | 0.80 | 34 | CL |
| 2 | 450 | 0.60 | 0.75 | 57 | NAG |
| 3 | 270 | 0.56 | 0.77 | 37 | empty |
| 4 | 328 | 0.53 | 0.74 | 53 | empty |
| 5 | 160 | 0.45 | 0.76 | 23 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1704 Ų buried · 10 hydrogen bonds · protein-protein
- L–H · 1678 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 866 Ų buried · 11 hydrogen bonds · protein-protein
- R–A · 729 Ų buried · 13 hydrogen bonds · protein-protein
- R–C · 591 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7R6X · SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2E12 Fab, S309 Fab, and… · the same entry in another collection · chain L against L, 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 7R6X · PDBe 7R6X · UniProt P0DTC2
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