Research workbench
Crystal structure of the vanr transcription factor in complex with vanillate
Analyse Crystal structure of the vanr transcription factor in complex with vanillate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z7B
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Padr family transcriptional regulator
- UniProt
- A0A0U4XX58
- Ligands
- VNL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Padr family transcriptional regulator | protein | 196 | 69% helix, 9% strand | A0A0U4XX58 |
| B | Padr family transcriptional regulator | protein | 197 | 70% helix, 10% strand | A0A0U4XX58 |
Ligands and binding sites
- VNL · 4-hydroxy-3-methoxybenzoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.73 | 0.79 | 84 | empty |
| 2 | 54 | 0.73 | 0.99 | 15 | VNL |
| 3 | 51 | 0.72 | 0.99 | 15 | VNL |
| 4 | 121 | 0.41 | 0.75 | 15 | empty |
| 5 | 80 | 0.38 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3360 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 5Z7B · Crystal structure of the VanR transcription factor in complex with vanillate · 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 A0A0U4XX58
- Elsewhere: RCSB PDB 5Z7B · PDBe 5Z7B · UniProt A0A0U4XX58
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