MolNFT v1 · #185605 · protein
Crystal structure of the multidrug binding transcriptional regulator lmrr in complex squaraine dye
7Q34 · Helix-turn-helix transcriptional regulator: “Crystal structure of the multidrug binding transcriptional regulator lmrr in complex squaraine dye”. X-ray diffraction, 2 ligands (8TF, NI), 7 pockets (best druggability 0.75). MolNFT v1…
- 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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