MolNFT v1 · #105693 · protein
1.9 ångström crystal structure of superantigen-like protein, exotoxin from staphylococcus aureus, in complex with sialyl-lewisx.
4RCO · Putative uncharacterized protein: “1.9 ångström crystal structure of superantigen-like protein, exotoxin from staphylococcus aureus, in complex…”. X-ray diffraction, 5 ligands (NDG, GAL, SIA), 3 pockets (best druggability 0.61).…
- PDB
- 4RCO
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q2G1S8
- Ligands
- NDG, GAL, SIA, FUC, CL
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein | protein | 192 | 19% helix, 43% strand | Q2G1S8 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.61 | 0.83 | 29 | CL |
| 2 | 99 | 0.40 | 0.76 | 14 | empty |
| 3 | 71 | 0.34 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RCO · 1.9 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2G1S8 · AlphaFold monomer V2.0 prediction for staphylococcal superantigen- like 4 (Q2G1S8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q2G1S8
- Elsewhere: RCSB PDB 4RCO · PDBe 4RCO · UniProt Q2G1S8
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