Research workbench
Crystal structure of the transcriptional regulator cadr from P. putida in complex with ZINC(II) and DNA
Analyse Crystal structure of the transcriptional regulator cadr from P. putida in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JNI
- Type
- protein + DNA
- Length
- 1,273 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadr; DNA (25-mer)
- UniProt
- Q93TP7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 10 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cadr | protein | 145 | 59% helix, 3% strand | Q93TP7 |
| B | Cadr | protein | 126 | 66% helix, 4% strand | Q93TP7 |
| C, F | Cadr | protein | 128 | 65% helix, 4% strand | Q93TP7 |
| E | Cadr | protein | 137 | 62% helix, 4% strand | Q93TP7 |
| G | Cadr | protein | 129 | 64% helix, 4% strand | Q93TP7 |
| H | Cadr | protein | 137 | 63% helix, 4% strand | Q93TP7 |
| I, M, O | DNA (25-mer) | dna | 25 | — | — |
| J, L, N | DNA (25-mer) | dna | 25 | — | — |
| K | DNA (25-mer) | dna | 24 | — | — |
| P | DNA (25-mer) | dna | 24 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.66 | 0.74 | 50 | empty |
| 2 | 707 | 0.64 | 0.74 | 69 | empty |
| 3 | 731 | 0.64 | 0.74 | 55 | empty |
| 4 | 82 | 0.64 | 0.91 | 24 | empty |
| 5 | 662 | 0.63 | 0.74 | 51 | empty |
Interfaces
39 interfaces between chains.
- G–H · 2359 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2350 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2345 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2336 Ų buried · 28 hydrogen bonds · protein-protein
- I–J · 1127 Ų buried · 108 hydrogen bonds · nucleic-nucleic
Compared structures
- 6JNI · Crystal structure of the transcriptional regulator CadR from P. putida in complex with… · 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 Q93TP7
- Elsewhere: RCSB PDB 6JNI · PDBe 6JNI · UniProt Q93TP7
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