Research workbench
Structure of sybody SR31 in complex with the SARS-cov-2 S receptor binding domain (rbd)
Analyse Structure of sybody SR31 in complex with the SARS-cov-2 S receptor binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D2Z
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SR31 against SARS-cov-2 rbd, non neutralizing; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC, BMA
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SR31 against SARS-cov-2 rbd, non neutralizing | protein | 117 | 8% helix, 54% strand | — |
| B | Spike protein S1 | protein | 212 | 19% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- FMT · Formic acid · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.63 | 0.86 | 29 | GOL, FMT |
Interfaces
1 interface between chains.
- A–B · 1478 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7D2Z · Structure of sybody SR31 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD) · 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 7D2Z · PDBe 7D2Z · UniProt P0DTC2
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