Research workbench
Crystal structure of receiver domain of kdpe D52A mutant from E. COLI
Analyse Crystal structure of receiver domain of kdpe D52A mutant from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L85
- Type
- protein
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kdp operon transcriptional regulatory protein kdpe
- UniProt
- P21866
- Ligands
- IOD
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kdp operon transcriptional regulatory protein kdpe | protein | 116 | 45% helix, 21% strand | P21866 |
| B | Kdp operon transcriptional regulatory protein kdpe | protein | 115 | 46% helix, 24% strand | P21866 |
| C | Kdp operon transcriptional regulatory protein kdpe | protein | 120 | 47% helix, 21% strand | P21866 |
Ligands and binding sites
- IOD · Iodide ion · ion · 35 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.62 | 0.84 | 22 | empty |
| 2 | 240 | 0.51 | 0.76 | 38 | IOD |
| 3 | 56 | 0.37 | 0.79 | 13 | IOD |
Interfaces
3 interfaces between chains.
- A–C · 799 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 51 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4L85 · Crystal structure of receiver domain of KdpE D52A mutant from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- P21866 · AlphaFold monomer V2.0 prediction for kdp operon transcriptional regulatory protein kdpe… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P21866
- Elsewhere: RCSB PDB 4L85 · PDBe 4L85 · UniProt P21866
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