Research workbench
Crystal structure of the desk-desr complex in the phosphatase state
Analyse Crystal structure of the desk-desr complex in the phosphatase state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IUN
- Type
- protein
- Length
- 1,042 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, BEF, MG, SO4
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 216 | 61% helix, 15% strand | O34757 |
| B | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 216 | 61% helix, 15% strand | O34757 |
| C | Transcriptional regulatory protein desr | protein | 131 | 40% helix, 23% strand | O34723 |
| D | Transcriptional regulatory protein desr | protein | 130 | 41% helix, 22% strand | O34723 |
| E | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 220 | 61% helix, 15% strand | O34757 |
| F | Transcriptional regulatory protein desr | protein | 129 | 41% helix, 23% strand | O34723 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 3 copies · chains A, B, E
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, C, B, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.74 | 0.81 | 72 | MES |
| 2 | 697 | 0.70 | 0.77 | 73 | empty |
| 3 | 174 | 0.67 | 0.87 | 25 | empty |
| 4 | 178 | 0.67 | 0.87 | 22 | empty |
| 5 | 180 | 0.62 | 0.84 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2197 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1148 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1117 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 968 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 306 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- O34723 · AlphaFold monomer V2.0 prediction for transcriptional regulatory protein desr (O34723) · a predicted model of the same protein · chain D 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 E against A, TM-score 0.58
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 5IUN · PDBe 5IUN · UniProt O34757 · UniProt O34723
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