MolNFT v1 · #152301 · protein + DNA
Crystal structure of the vibrio cholera vqma-ligand-DNA complex provides molecular mechanisms for drug design
6IDE · Transcriptional regulator luxr family: “Crystal structure of the vibrio cholera vqma-ligand-DNA complex provides molecular mechanisms for drug design”. X-ray diffraction, 1 ligand (A1U), 8 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6IDE
- Type
- protein + DNA
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator luxr family; DNA (5'…
- UniProt
- A0A0H6WEL7
- Ligands
- A1U
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator luxr family | protein | 226 | 41% helix, 22% strand | A0A0H6WEL7 |
| B | Transcriptional regulator luxr family | protein | 228 | 43% helix, 21% strand | A0A0H6WEL7 |
| C | DNA (5'- D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- A1U · 3,5-dimethylpyrazin-2-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.75 | 0.83 | 60 | empty |
| 2 | 263 | 0.52 | 0.75 | 41 | empty |
| 3 | 189 | 0.51 | 0.78 | 27 | empty |
| 4 | 193 | 0.51 | 0.77 | 26 | empty |
| 5 | 223 | 0.51 | 0.76 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3403 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 818 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- B–D · 372 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 368 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 357 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6IDE · Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular… · 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 A0A0H6WEL7
- Elsewhere: RCSB PDB 6IDE · PDBe 6IDE · UniProt A0A0H6WEL7
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