Research workbench
Crystal structure of phosphorylated deskc in complex with AMP-pcp
Analyse Crystal structure of phosphorylated deskc in complex with AMP-pcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GIG
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor histidine kinase desk
- EC
- 2.7.13.3
- UniProt
- O34757
- Ligands
- ACP, MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 212 | 59% helix, 16% strand | O34757 |
| B | Sensor histidine kinase desk (EC 2.7.13.3) | protein | 205 | 60% helix, 16% strand | O34757 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.59 | 0.87 | 26 | ACP |
| 2 | 267 | 0.59 | 0.78 | 31 | empty |
| 3 | 112 | 0.58 | 0.85 | 20 | empty |
| 4 | 149 | 0.55 | 0.82 | 28 | ACP |
| 5 | 103 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2096 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3GIG · Crystal structure of phosphorylated DesKC in complex with AMP-PCP · the same entry in another collection · chain A against A, TM-score 1.00
- O34757 · AlphaFold monomer V2.0 prediction for sensor histidine kinase desk (O34757) · a predicted model of the same protein · chain A 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
- Elsewhere: RCSB PDB 3GIG · PDBe 3GIG · UniProt O34757
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