Research workbench
Crystal structure of prfa-DNA binary complex
Analyse Crystal structure of prfa-DNA binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X6E
- Type
- protein + DNA
- Length
- 1,588 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Listeriolysin positive regulatory factor a; DNA (29-mer); DNA (28-mer)
- UniProt
- Q4TVQ0
- Ligands
- GSH
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, N, A, B, E, F | Listeriolysin positive regulatory factor a | protein | 236 | 40% helix, 26% strand | Q4TVQ0 |
| O, C | DNA (29-mer) | dna | 29 | — | — |
| P | DNA (28-mer) | dna | 28 | — | — |
| D, H | DNA (28-mer) | dna | 29 | — | — |
| G | DNA (29-mer) | dna | 28 | — | — |
Ligands and binding sites
- GSH · Glutathione · ligand · 6 copies · chains M, N, A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.79 | 0.81 | 94 | GSH |
| 2 | 1069 | 0.75 | 0.78 | 118 | empty |
| 3 | 72 | 0.74 | 0.98 | 20 | empty |
| 4 | 63 | 0.73 | 0.98 | 17 | empty |
| 5 | 667 | 0.72 | 0.79 | 80 | empty |
Interfaces
24 interfaces between chains.
- M–N · 2406 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2385 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 2359 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1253 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- O–P · 1243 Ų buried · 129 hydrogen bonds · nucleic-nucleic
Compared structures
- 5X6E · Crystal structure of PrfA-DNA binary complex · the same entry in another collection · chain B against B, 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 5X6E · PDBe 5X6E · UniProt Q4TVQ0
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