MolNFT v1 · #75350 · protein
Crystal structure of E.COLI dha kinase dhak-dhal complex
3PNL · Pts-dependent dihydroxyacetone kinase, dihydroxyacetone…: “Crystal structure of E.COLI dha kinase dhak-dhal complex”. X-ray diffraction, 2 ligands (ADP, MG), 3 pockets (best druggability 0.79). MolNFT v1 #75350 on GenesisL1: 3D…
- PDB
- 3PNL
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- 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, P76014
- Ligands
- ADP, MG
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-) | protein | 356 | 31% helix, 30% strand | P76015 |
| B | Pts-dependent dihydroxyacetone kinase, ADP-binding subunit dhal (EC 2.7.-.-) | protein | 211 | 74% helix, 3% strand | P76014 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.79 | 0.85 | 73 | ADP, MG |
| 2 | 268 | 0.62 | 0.80 | 40 | empty |
| 3 | 142 | 0.51 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1272 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3PNL · Crystal Structure of E.coli Dha kinase DhaK-DhaL complex · the same entry in another collection · chain A against A, TM-score 1.00
- P76014 · AlphaFold monomer V2.0 prediction for pep-dependent dihydroxyacetone kinase, ADP-binding… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P76015 · AlphaFold monomer V2.0 prediction for pep-dependent dihydroxyacetone kinase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P76014
- Elsewhere: RCSB PDB 3PNL · PDBe 3PNL · UniProt P76015 · UniProt P76014
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