Research workbench
The transcriptional regulator prfa-A94V mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif
Analyse The transcriptional regulator prfa-A94V 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
- 6QWF
- Type
- protein + DNA
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin positive regulatory factor a; DNA (30-mer)
- UniProt
- Q4TVQ0
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Listeriolysin positive regulatory factor a | protein | 236 | 45% helix, 25% strand | Q4TVQ0 |
| C | DNA (30-mer) | dna | 30 | — | — |
| D | DNA (30-mer) | dna | 30 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.98 | 18 | empty |
| 2 | 566 | 0.71 | 0.80 | 64 | empty |
| 3 | 51 | 0.70 | 0.98 | 18 | empty |
| 4 | 304 | 0.68 | 0.82 | 35 | GOL |
| 5 | 315 | 0.67 | 0.81 | 33 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 2361 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1314 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- B–C · 386 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 375 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 348 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6QWF · The Transcriptional Regulator PrfA-A94V mutant from Listeria Monocytogenes in complex… · 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 6QWF · PDBe 6QWF · UniProt Q4TVQ0
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