Research workbench
Crystal structure of E.COLI dha kinase dhak (H56N) complex with dha
Analyse Crystal structure of E.COLI dha kinase dhak (H56N) complex with dha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNQ
- Type
- protein
- Length
- 1,339 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
- Ligands
- 2HA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-) | protein | 334 | 32% helix, 31% strand | P76015 |
| B | Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-) | protein | 336 | 32% helix, 32% strand | P76015 |
| C | Pts-dependent dihydroxyacetone kinase, dihydroxyacetone- binding subunit dhak (EC 2.7.-.-) | protein | 335 | 32% helix, 30% strand | P76015 |
Ligands and binding sites
- 2HA · Dihydroxyacetone · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.83 | 0.84 | 107 | empty |
| 2 | 1032 | 0.81 | 0.82 | 81 | empty |
| 3 | 81 | 0.64 | 0.91 | 26 | empty |
| 4 | 176 | 0.51 | 0.78 | 36 | empty |
| 5 | 128 | 0.47 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1343 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3PNQ · Crystal Structure of E.coli Dha kinase DhaK (H56N) complex with Dha · 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
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
- Elsewhere: RCSB PDB 3PNQ · PDBe 3PNQ · UniProt P76015
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