MolNFT v1 · #153725 · protein + DNA
Crystal structure of the transcriptional regulator cadr from P. putida in complex with ZINC(II) and DNA
6JNI: “Crystal structure of the transcriptional regulator cadr from P. putida in complex with ZINC(II) and DNA”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.66). MolNFT v1 #153725 on GenesisL1: 3D structure, binding…
- 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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