MolNFT v1 · #105782 · protein
1.93 ångström crystal structure of superantigen-like protein from staphylococcus aureus in complex with sialyl-lewis X.
4RFB · Putative uncharacterized protein: “1.93 ångström crystal structure of superantigen-like protein from staphylococcus aureus in complex with…”. X-ray diffraction, 5 ligands (NAG, GAL, SIA), 4 pockets (best druggability 0.78). MolNFT…
- PDB
- 4RFB
- Type
- protein
- Length
- 770 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q2G1S5
- Ligands
- NAG, GAL, SIA, FUC, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 194 | 18% helix, 41% strand | Q2G1S5 |
| B | Putative uncharacterized protein | protein | 192 | 19% helix, 42% strand | Q2G1S5 |
| C | Putative uncharacterized protein | protein | 191 | 18% helix, 41% strand | Q2G1S5 |
| D | Putative uncharacterized protein | protein | 193 | 18% helix, 45% strand | Q2G1S5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, C
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, D, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, D, B, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, D, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C
- PGE · Triethylene glycol · additive · chains B
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.78 | 0.85 | 68 | empty |
| 2 | 765 | 0.76 | 0.80 | 71 | empty |
| 3 | 489 | 0.73 | 0.82 | 58 | GAL, FUC |
| 4 | 218 | 0.44 | 0.73 | 35 | GAL, SIA, FUC |
Interfaces
5 interfaces between chains.
- A–B · 758 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 686 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RFB · 1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus… · 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 Q2G1S5
- Elsewhere: RCSB PDB 4RFB · PDBe 4RFB · UniProt Q2G1S5
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