Research workbench
The transcriptional regulator prfa from listeria monocytogenes in complex with a 30-bp operator prfa-box motif
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
- 5LEJ
- Type
- protein + DNA
- Length
- 533 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin regulatory protein; DNA (30-mer)
- UniProt
- P22262
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Listeriolysin regulatory protein | protein | 236 | 45% helix, 25% strand | P22262 |
| B | Listeriolysin regulatory protein | protein | 237 | 47% helix, 23% strand | P22262 |
| C | DNA (30-mer) | dna | 30 | — | — |
| D | DNA (30-mer) | dna | 30 | — | — |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.76 | 0.98 | 21 | empty |
| 2 | 691 | 0.72 | 0.79 | 79 | empty |
| 3 | 319 | 0.67 | 0.81 | 34 | empty |
| 4 | 308 | 0.66 | 0.81 | 34 | empty |
| 5 | 87 | 0.44 | 0.80 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2383 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1310 Ų buried · 125 hydrogen bonds · nucleic-nucleic
- A–D · 383 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 380 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 333 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5LEJ · The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a 30-bp… · 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 A against A, TM-score 0.97
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 5LEJ · PDBe 5LEJ · UniProt P22262
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