Research workbench
The transcriptional regulator prfa-G145S mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif
Analyse The transcriptional regulator prfa-G145S mutant from listeria monocytogenes in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LEK
- Type
- protein + DNA
- Length
- 532 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
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Listeriolysin regulatory protein | protein | 236 | 45% helix, 25% strand | P22262 |
| C | DNA (30-mer) | dna | 30 | — | — |
| D | DNA (30-mer) | dna | 30 | — | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.77 | 0.99 | 20 | empty |
| 2 | 584 | 0.72 | 0.80 | 75 | empty |
| 3 | 62 | 0.72 | 0.97 | 25 | empty |
| 4 | 312 | 0.66 | 0.81 | 37 | empty |
| 5 | 252 | 0.65 | 0.82 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2400 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1307 Ų buried · 117 hydrogen bonds · nucleic-nucleic
- A–D · 381 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 380 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 336 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5LEK · The Transcriptional Regulator PrfA-G145S mutant from Listeria Monocytogenes in complex… · 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 5LEK · PDBe 5LEK · UniProt P22262
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