Research workbench
Crystal structure of the transcriptional regulator cadr from P. putida in complex with CADMIUM(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
- 6JGX
- Type
- protein + DNA
- Length
- 323 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadr; DNA (5'- D(*CP*AP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*GP*CP*TP*AP*CP*AP*GP*GP*GP*T)- 3')…
- UniProt
- Q93TP7
- Ligands
- CD
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadr | protein | 143 | 58% helix, 3% strand | Q93TP7 |
| B | Cadr | protein | 136 | 61% helix, 4% strand | Q93TP7 |
| C | DNA (5'- D(*CP*AP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*GP*CP*TP*AP*CP*AP*GP*GP*GP*T)- 3') | dna | 22 | — | — |
| D | DNA (5'- D(*GP*AP*CP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*CP*TP*AP*TP*AP*GP*GP*GP*T)- 3') | dna | 22 | — | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 597 | 0.61 | 0.74 | 58 | empty |
| 2 | 310 | 0.49 | 0.73 | 28 | empty |
| 3 | 103 | 0.39 | 0.76 | 18 | empty |
| 4 | 57 | 0.29 | 0.75 | 15 | empty |
| 5 | 50 | 0.26 | 0.74 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2347 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 965 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- A–C · 414 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 413 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 381 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6JGX · 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 6JGX · PDBe 6JGX · UniProt Q93TP7
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