Research workbench
Crystal structure of the desk-desr complex in the phosphotransfer state with high MG2+ (150 mm)
Analyse Crystal structure of the desk-desr complex in the phosphotransfer state with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IUK
- Type
- protein
- Length
- 1,100 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor histidine kinase desk; Transcriptional regulatory protein desr
- EC
- 2.7.13.3
- UniProt
- O34757, O34723
- Ligands
- ACP, MG, K
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 209 | 62% helix, 16% strand | O34757 |
| B | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 207 | 62% helix, 16% strand | O34757 |
| D | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 213 | 60% helix, 15% strand | O34757 |
| E | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 206 | 62% helix, 16% strand | O34757 |
| C | Transcriptional regulatory protein desr | protein | 132 | 38% helix, 23% strand | O34723 |
| F | Transcriptional regulatory protein desr | protein | 133 | 39% helix, 23% strand | O34723 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, D, E, C
- K · Potassium ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.73 | 0.78 | 65 | empty |
| 2 | 987 | 0.73 | 0.76 | 83 | empty |
| 3 | 272 | 0.57 | 0.77 | 32 | empty |
| 4 | 85 | 0.56 | 0.86 | 22 | ACP |
| 5 | 109 | 0.55 | 0.84 | 21 | ACP |
Interfaces
8 interfaces between chains.
- D–E · 2502 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2413 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 765 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 760 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 546 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5IUK · Crystal structure of the DesK-DesR complex in the phosphotransfer state with high Mg2+… · the same entry in another collection · chain F against F, TM-score 1.00
- O34723 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein desr (O34723) · a predicted model of the same protein · chain F against A, TM-score 0.96
- O34757 · AlphaFold monomer V2.0 prediction for sensor histidine kinase desk (O34757) · a predicted model of the same protein · chain D against A, TM-score 0.61
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 O34757
- Every structure of UniProt O34723
- Elsewhere: RCSB PDB 5IUK · PDBe 5IUK · UniProt O34757 · UniProt O34723
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