MolNFT v1 · #50274 · protein
Crystal structure of staphylococcal superantigen-like protein 11 in complex with sialyl lewis X
2RDG: “Crystal structure of staphylococcal superantigen-like protein 11 in complex with sialyl lewis X”. X-ray diffraction, 5 ligands (NDG, GAL, SIA), 1 pocket (best druggability 0.36). MolNFT v1 #50274 on GenesisL1: 3D structure, binding…
- PDB
- 2RDG
- Type
- protein
- Length
- 192 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superantigen-like protein 11
- UniProt
- A8E1U5
- Ligands
- NDG, GAL, SIA, FUC, K
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superantigen-like protein 11 | protein | 192 | 20% helix, 44% strand | A8E1U5 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- K · Potassium ion · metal · 3 copies · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.36 | 0.80 | 14 | empty |
Compared structures
- 2RDG · Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with Sialyl… · the same entry in another collection · chain A against A, TM-score 1.00
- A8E1U5 · AlphaFold monomer V2.0 prediction for superantigen-like protein 11 (A8E1U5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A8E1U5
- Elsewhere: RCSB PDB 2RDG · PDBe 2RDG · UniProt A8E1U5
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