MolNFT v1 · #153520 · protein + DNA
Crystal structure of the transcriptional regulator cadr from P. putida in complex with DNA
6JGW: “Crystal structure of the transcriptional regulator cadr from P. putida in complex with DNA”. X-ray diffraction, 5 pockets (best druggability 0.66). MolNFT v1 #153520 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JGW
- Type
- protein + DNA
- Length
- 295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadr; DNA (27-mer)
- UniProt
- Q93TP7
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cadr | protein | 116 | 71% helix, 3% strand | Q93TP7 |
| A | Cadr | protein | 125 | 70% helix, 3% strand | Q93TP7 |
| C | DNA (27-mer) | dna | 27 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.66 | 0.76 | 60 | empty |
| 2 | 57 | 0.36 | 0.79 | 13 | empty |
| 3 | 56 | 0.32 | 0.77 | 11 | empty |
| 4 | 67 | 0.30 | 0.75 | 11 | empty |
| 5 | 63 | 0.26 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1924 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1196 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- A–C · 474 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 468 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 373 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6JGW · Crystal structure of the transcriptional regulator CadR from P. putida in complex with DNA · 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 Q93TP7
- Elsewhere: RCSB PDB 6JGW · PDBe 6JGW · UniProt Q93TP7
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