MolNFT v1 · #186227 · protein
SARS-cov-2 spike receptor-binding domain (rbd) in complex with S2X35 Fab and S309 Fab
7R6W · Light chain of Fab domain of monoclonal antibody S309: “SARS-cov-2 spike receptor-binding domain (rbd) in complex with S2X35 Fab and S309 Fab”. X-ray diffraction, 3 ligands (NAG, SO4, CL), 11 pockets (best druggability 0.65). MolNFT…
- PDB
- 7R6W
- Type
- protein
- Length
- 1,074 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab domain of monoclonal antibody S309; Heavy chain of Fab domain of…
- UniProt
- P0DTC2
- Ligands
- NAG, SO4, CL
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Light chain of Fab domain of monoclonal antibody S309 | protein | 213 | 7% helix, 50% strand | — |
| A | Heavy chain of Fab domain of monoclonal antibody S309 | protein | 221 | 8% helix, 51% strand | — |
| L | Light chain of Fab domain of monoclonal antibody S2X35 | protein | 215 | 8% helix, 52% strand | — |
| H | Heavy chain of Fab domain of monoclonal antibody S2X35 | protein | 230 | 9% helix, 52% strand | — |
| R | Spike protein S1 | protein | 195 | 18% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A, R
- SO4 · Sulfate ion · ion · 23 copies · chains B, A, L, H, R
- CL · Chloride ion · ion · 3 copies · chains B, A, H, L, R
- GOL · Glycerol · additive · 3 copies · chains B, A
- POL · N-propanol · additive · 2 copies · chains H, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.65 | 0.75 | 56 | empty |
| 2 | 277 | 0.54 | 0.75 | 34 | NAG |
| 3 | 348 | 0.53 | 0.74 | 52 | empty |
| 4 | 128 | 0.45 | 0.77 | 27 | empty |
| 5 | 126 | 0.41 | 0.75 | 22 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1818 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 1667 Ų buried · 13 hydrogen bonds · protein-protein
- H–R · 730 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 652 Ų buried · 11 hydrogen bonds · protein-protein
- L–R · 319 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7R6W · SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab · the same entry in another collection · chain B against B, 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 7R6W · PDBe 7R6W · UniProt P0DTC2
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