MolNFT v1 · #148123 · protein
The transcriptional regulator prfa from listeria monocytogenes in complex with a ring-fused 2-pyridone (MK202)
6EXM · Listeriolysin positive regulatory factor a: “The transcriptional regulator prfa from listeria monocytogenes in complex with a ring-fused 2-pyridone (MK202)”. X-ray diffraction, 2 ligands (QQH, NA), 4 pockets (best druggability…
- PDB
- 6EXM
- Type
- protein
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin positive regulatory factor a
- UniProt
- Q4TVQ0
- Ligands
- QQH, NA
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Listeriolysin positive regulatory factor a | protein | 236 | 46% helix, 28% strand | Q4TVQ0 |
| B | Listeriolysin positive regulatory factor a | protein | 229 | 46% helix, 28% strand | Q4TVQ0 |
Ligands and binding sites
- QQH · [(3~{R})-3-carboxy-7-[(2,3-dimethylphenyl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.78 | 0.89 | 31 | QQH |
| 2 | 352 | 0.75 | 0.86 | 31 | QQH |
| 3 | 538 | 0.75 | 0.82 | 54 | empty |
| 4 | 55 | 0.57 | 0.90 | 15 | IPA |
Interfaces
1 interface between chains.
- A–B · 2151 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6EXM · 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
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 Q4TVQ0
- Elsewhere: RCSB PDB 6EXM · PDBe 6EXM · UniProt Q4TVQ0
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