Research workbench
1.75 ångström crystal structure of superantigen-like protein, exotoxin from staphylococcus aureus, in complex with sialyl-lewisx.
Analyse 1.75 ångström crystal structure of superantigen-like protein, exotoxin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I4D
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superantigen-like protein
- UniProt
- A0A0D6GBT0
- Ligands
- NDG, GAL, SIA, FUC, NAG
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superantigen-like protein | protein | 192 | 18% helix, 41% strand | A0A0D6GBT0 |
| B | Superantigen-like protein | protein | 193 | 18% helix, 41% strand | A0A0D6GBT0 |
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.38 | 0.74 | 21 | GAL, FUC |
| 2 | 61 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5I4D · 1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from… · 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 A0A0D6GBT0
- Elsewhere: RCSB PDB 5I4D · PDBe 5I4D · UniProt A0A0D6GBT0
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