Research workbench
Crystal structure of the E.COLI DHAR(N)-DHAK(T79L) complex
Analyse Crystal structure of the E.COLI DHAR(N)-DHAK(T79L) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LRY
- Type
- protein
- Length
- 1,300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak…
- EC
- 2.7.-.-
- UniProt
- P76015, P76016
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-) | protein | 356 | 30% helix, 30% strand | P76015 |
| C, D | Pts-dependent dihydroxyacetone kinase operon regulatory protein | protein | 294 | 43% helix, 28% strand | P76016 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.83 | 0.84 | 106 | empty |
| 2 | 816 | 0.80 | 0.83 | 86 | GOL |
| 3 | 433 | 0.63 | 0.77 | 54 | empty |
| 4 | 216 | 0.49 | 0.75 | 23 | empty |
| 5 | 78 | 0.41 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2410 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2064 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1178 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4LRY · Crystal Structure of the E.coli DhaR(N)-DhaK(T79L) complex · the same entry in another collection · chain D against D, TM-score 1.00
- P76015 · AlphaFold monomer V2.0 prediction for pep-dependent dihydroxyacetone kinase… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P76016 · AlphaFold monomer V2.0 prediction for pts-dependent dihydroxyacetone kinase operon… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P76015
- Every structure of UniProt P76016
- Elsewhere: RCSB PDB 4LRY · PDBe 4LRY · UniProt P76015 · UniProt P76016
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