Research workbench
Crystal structure of the multidrug binding transcriptional regulator lmrr in complex squaraine dye
Analyse Crystal structure of the multidrug binding transcriptional regulator lmrr in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q34
- Type
- protein
- Length
- 392 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helix-turn-helix transcriptional regulator
- UniProt
- A0A0A7SZD7
- Ligands
- 8TF, NI
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helix-turn-helix transcriptional regulator | protein | 101 | 62% helix, 13% strand | A0A0A7SZD7 |
| B | Helix-turn-helix transcriptional regulator | protein | 98 | 68% helix, 7% strand | A0A0A7SZD7 |
| C | Helix-turn-helix transcriptional regulator | protein | 105 | 64% helix, 10% strand | A0A0A7SZD7 |
| D | Helix-turn-helix transcriptional regulator | protein | 88 | 73% helix, 2% strand | A0A0A7SZD7 |
Ligands and binding sites
- 8TF · 2,4-bis[(e)-(1-ethyl-3,3-dimethyl-indol-2-ylidene) methyl]cyclobutane-1,3-dione · ligand · 2 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.75 | 0.78 | 56 | 8TF |
| 2 | 918 | 0.70 | 0.75 | 60 | 8TF |
| 3 | 156 | 0.54 | 0.80 | 19 | empty |
| 4 | 92 | 0.39 | 0.77 | 19 | empty |
| 5 | 62 | 0.35 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1325 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1293 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7Q34 · Crystal structure of the multidrug binding transcriptional regulator LmrR in complex… · 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 A0A0A7SZD7
- Elsewhere: RCSB PDB 7Q34 · PDBe 7Q34 · UniProt A0A0A7SZD7
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