Research workbench
The transcriptional regulator prfa from listeria monocytogenes in complex with a ring-fused 2-pyridone (KSK67)
Analyse The transcriptional regulator prfa from listeria monocytogenes in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EUT
- Type
- protein
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin regulatory protein
- UniProt
- P22262
- Ligands
- BY8, NA
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Listeriolysin regulatory protein | protein | 236 | 46% helix, 27% strand | P22262 |
| B | Listeriolysin regulatory protein | protein | 229 | 47% helix, 25% strand | P22262 |
Ligands and binding sites
- BY8 · (3~{R})-8-cyclopropyl-7-[(4-methylnaphthalen-1-yl) methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.82 | 0.83 | 84 | BY8 |
| 2 | 345 | 0.78 | 0.87 | 31 | BY8 |
Interfaces
1 interface between chains.
- A–B · 2168 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6EUT · The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P22262 · AlphaFold monomer V2.0 prediction for listeriolysin regulatory protein (P22262) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P22262
- Elsewhere: RCSB PDB 6EUT · PDBe 6EUT · UniProt P22262
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