MolNFT v1 · #139145 · protein + DNA
Crystal structure of prfa-DNA binary complex
5X6D · Listeriolysin positive regulatory factor a: “Crystal structure of prfa-DNA binary complex”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #139145 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X6D
- Type
- protein + DNA
- Length
- 1,586 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
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H, N | Listeriolysin positive regulatory factor a | protein | 236 | 44% helix, 25% strand | Q4TVQ0 |
| C, K, P | DNA (29-mer) | dna | 29 | — | — |
| D, L | DNA (28-mer) | dna | 28 | — | — |
| G, M | Listeriolysin positive regulatory factor a | protein | 235 | 37% helix, 18% strand | Q4TVQ0 |
| O | DNA (28-mer) | dna | 29 | — | — |
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 | 72 | 0.75 | 0.98 | 20 | empty |
| 2 | 753 | 0.74 | 0.79 | 93 | empty |
| 3 | 893 | 0.73 | 0.78 | 98 | empty |
| 4 | 57 | 0.73 | 0.99 | 18 | empty |
| 5 | 65 | 0.72 | 0.97 | 19 | empty |
Interfaces
25 interfaces between chains.
- M–N · 2376 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2337 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 2315 Ų buried · 6 hydrogen bonds · protein-protein
- O–P · 1229 Ų buried · 134 hydrogen bonds · nucleic-nucleic
- L–K · 1221 Ų buried · 113 hydrogen bonds · nucleic-nucleic
Compared structures
- 5X6D · Crystal structure of PrfA-DNA binary 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 5X6D · PDBe 5X6D · UniProt Q4TVQ0
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