MolNFT v1 · #154057 · protein + DNA
Crystal structure of the transcription regulator cadr N81M mutant from P. putida in complex with CADMIUM(II) and DNA
6JYW: “Crystal structure of the transcription regulator cadr N81M mutant from P. putida in complex with CADMIUM(II)…”. X-ray diffraction, 1 ligand (CD), 4 pockets (best druggability 0.63). MolNFT v1 #154057 on GenesisL1: 3D structure…
- PDB
- 6JYW
- Type
- protein + DNA
- Length
- 315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadr; DNA (5'- D(*AP*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
- 4 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadr | protein | 139 | 60% helix, 4% strand | Q93TP7 |
| B | Cadr | protein | 132 | 64% helix, 4% strand | Q93TP7 |
| C | DNA (5'- D(*AP*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(*TP*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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.63 | 0.75 | 72 | empty |
| 2 | 50 | 0.36 | 0.80 | 13 | empty |
| 3 | 127 | 0.36 | 0.73 | 16 | empty |
| 4 | 104 | 0.33 | 0.72 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2350 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 956 Ų buried · 106 hydrogen bonds · nucleic-nucleic
- A–D · 427 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 425 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 349 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6JYW · Crystal structure of the transcription regulator CadR N81M mutant from P. putida in… · 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 6JYW · PDBe 6JYW · UniProt Q93TP7
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