Research workbench
The evolving story of AtzT, a periplasmic binding protein
Analyse The evolving story of AtzT, a periplasmic binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PI6
- Type
- protein
- Length
- 1,328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Pseudomonas sp. (strain ADP)
- Molecule
- Atrazine periplasmic binding protein
- UniProt
- Q936X6
- Ligands
- OKM
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.65 · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Atrazine periplasmic binding protein | protein | 333 | 41% helix, 23% strand | Q936X6 |
| C, D | Atrazine periplasmic binding protein | protein | 331 | 41% helix, 23% strand | Q936X6 |
Ligands and binding sites
- OKM · 4-(ethylamino)-6-[(propan-2-yl)amino]-1,3,5-triazin-2-ol · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.81 | 0.82 | 102 | empty |
| 2 | 1154 | 0.75 | 0.77 | 109 | empty |
| 3 | 277 | 0.69 | 0.84 | 40 | empty |
| 4 | 177 | 0.62 | 0.83 | 34 | empty |
| 5 | 133 | 0.60 | 0.85 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–D · 552 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6PI6 · The evolving story of atzt, a periplasmic binding protein · 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 Q936X6
- Elsewhere: RCSB PDB 6PI6 · PDBe 6PI6 · UniProt Q936X6
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