MolNFT v1 · #153521 · protein + DNA
Crystal structure of the transcriptional regulator cadr from P. putida in complex with CADMIUM(II) and DNA
6JGX: “Crystal structure of the transcriptional regulator cadr from P. putida in complex with CADMIUM(II) and DNA”. X-ray diffraction, 1 ligand (CD), 5 pockets (best druggability 0.61). MolNFT v1 #153521 on GenesisL1: 3D structure, binding…
- 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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