MolNFT v1 · #126065 · protein
The transcriptional regulator prfa from listeria monocytogenes in complex with glutathione
5LRR · Listeriolysin positive regulatory factor a: “The transcriptional regulator prfa from listeria monocytogenes in complex with glutathione”. X-ray diffraction, 3 ligands (GSH, NA, PI), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5LRR
- Type
- protein
- Length
- 1,871 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin positive regulatory factor a
- UniProt
- Q4TVQ0
- Ligands
- GSH, NA, PI
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G | Listeriolysin positive regulatory factor a | protein | 236 | 46% helix, 27% strand | Q4TVQ0 |
| F | Listeriolysin positive regulatory factor a | protein | 226 | 44% helix, 27% strand | Q4TVQ0 |
| H | Listeriolysin positive regulatory factor a | protein | 229 | 47% helix, 28% strand | Q4TVQ0 |
Ligands and binding sites
- GSH · Glutathione · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 5 copies · chains A, D, E, F, H
- PI · Hydrogenphosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.82 | 0.88 | 64 | GSH |
| 2 | 645 | 0.82 | 0.86 | 81 | empty |
| 3 | 480 | 0.78 | 0.85 | 50 | GSH |
| 4 | 905 | 0.77 | 0.80 | 103 | empty |
| 5 | 480 | 0.76 | 0.84 | 57 | GSH |
Interfaces
16 interfaces between chains.
- G–H · 2351 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2336 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2300 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2248 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 686 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5LRR · The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with glutathione · 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 5LRR · PDBe 5LRR · UniProt Q4TVQ0
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