Research workbench
Crystal structure of the D100R multidrug binding transcriptional regulator lmrr in complex with rhodium bis-diphosphine complex
Analyse Crystal structure of the D100R multidrug binding transcriptional regulator lmrr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VWE
- 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 0.59
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, padr-like family | protein | 103 | 66% helix, 11% strand | A2RI36 |
| B | Transcriptional regulator, padr-like family | protein | 104 | 63% helix, 13% 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 | 482 | 0.59 | 0.73 | 35 | JY1 |
| 2 | 211 | 0.46 | 0.73 | 20 | empty |
| 3 | 76 | 0.33 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1323 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VWE · Crystal structure of the D100R multidrug binding transcriptional regulator LmrR 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 A2RI36
- Elsewhere: RCSB PDB 6VWE · PDBe 6VWE · UniProt A2RI36
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