MolNFT v1 · #146651 · protein
Crystal structure of the multidrug binding transcriptional regulator lmrr in complex with rhodium bis-diphosphine complex
6DO0 · Transcriptional regulator, padr-like family: “Crystal structure of the multidrug binding transcriptional regulator lmrr in complex with rhodium…”. X-ray diffraction, 1 ligand (JY1), 3 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 6DO0
- Type
- protein
- Length
- 207 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, padr-like family
- UniProt
- A2RI36
- Ligands
- JY1
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, padr-like family | protein | 100 | 59% helix, 11% strand | A2RI36 |
| B | Transcriptional regulator, padr-like family | protein | 107 | 63% helix, 10% strand | A2RI36 |
Ligands and binding sites
- JY1 · Bis[diethyl(methyl)-lambda~5~-phosphanyl]{bis[{[(2-{[2-(2,5-dioxopyrrolidin-1-yl)ethyl]amino}-2-oxoethyl) amino]methyl}(diethyl)-lambda~5~-phosphanyl]}rhodium · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.65 | 0.74 | 56 | JY1 |
| 2 | 90 | 0.36 | 0.75 | 18 | empty |
| 3 | 50 | 0.27 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1330 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6DO0 · Crystal structure of the multidrug binding transcriptional regulator LmrR 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 A2RI36
- Elsewhere: RCSB PDB 6DO0 · PDBe 6DO0 · UniProt A2RI36
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