MolNFT v1 · #122616 · protein
Crystal structure of the desk-desr complex in the phosphotransfer state with high MG2+ (150 mm) and BEF3
5IUL · Sensor histidine kinase desk: “Crystal structure of the desk-desr complex in the phosphotransfer state with high MG2+ (150 mm) and BEF3”. X-ray diffraction, 3 ligands (ACP, MG, K), 16 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 5IUL
- Type
- protein
- Length
- 1,102 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
- 16 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 211 | 61% helix, 16% strand | O34757 |
| B | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 207 | 59% helix, 16% strand | O34757 |
| C | Transcriptional regulatory protein desr | protein | 132 | 40% helix, 23% strand | O34723 |
| D | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 213 | 59% helix, 15% strand | O34757 |
| E | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 207 | 60% helix, 16% strand | O34757 |
| F | Transcriptional regulatory protein desr | protein | 132 | 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 · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.67 | 0.77 | 45 | empty |
| 2 | 527 | 0.63 | 0.75 | 52 | empty |
| 3 | 253 | 0.60 | 0.80 | 23 | empty |
| 4 | 410 | 0.59 | 0.75 | 39 | empty |
| 5 | 114 | 0.54 | 0.83 | 23 | ACP, MG |
Interfaces
8 interfaces between chains.
- D–E · 2469 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2390 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 770 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 746 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 585 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5IUL · 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 0.97
- 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 5IUL · PDBe 5IUL · UniProt O34757 · UniProt O34723
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