Research workbench
Crystal structure of the effector-binding domain of dasr (dasr-ebd) in complex with N-acetylglucosamine-6-phosphate
Analyse Crystal structure of the effector-binding domain of dasr (dasr-ebd) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZSK
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor dasr
- UniProt
- Q9K492
- Ligands
- 16G, 4QY
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional repressor dasr | protein | 166 | 21% helix, 48% strand | Q9K492 |
| B | Hth-type transcriptional repressor dasr | protein | 165 | 22% helix, 48% strand | Q9K492 |
Ligands and binding sites
- 16G · 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- 4QY · 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose · ligand · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.77 | 0.98 | 28 | 16G |
| 2 | 97 | 0.76 | 0.97 | 26 | 4QY |
| 3 | 52 | 0.34 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1560 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4ZSK · Crystal structure of the effector-binding domain of DasR (DasR-EBD) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9K492 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor dasr (Q9K492) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9K492
- Elsewhere: RCSB PDB 4ZSK · PDBe 4ZSK · UniProt Q9K492
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