Research workbench
Crystal structure of the photoactive yellow protein domain from the sensor histidine kinase ppr from rhodospirillum centenum
Analyse Crystal structure of the photoactive yellow protein domain from the sensor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MZU
- Type
- protein
- Length
- 329 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ppr
- UniProt
- Q9X2W8
- Ligands
- HC4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ppr | protein | 107 | 32% helix, 36% strand | Q9X2W8 |
| B | Ppr | protein | 114 | 32% helix, 32% strand | Q9X2W8 |
| C | Ppr | protein | 108 | 35% helix, 28% strand | Q9X2W8 |
Ligands and binding sites
- HC4 · 4'-hydroxycinnamic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.69 | 0.87 | 31 | empty |
| 2 | 221 | 0.60 | 0.80 | 22 | HC4 |
| 3 | 52 | 0.56 | 0.90 | 14 | HC4 |
| 4 | 53 | 0.55 | 0.89 | 14 | HC4 |
Interfaces
2 interfaces between chains.
- B–C · 469 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 188 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1MZU · Crystal Structure of the Photoactive Yellow Protein Domain from the Sensor Histidine… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9X2W8
- Elsewhere: RCSB PDB 1MZU · PDBe 1MZU · UniProt Q9X2W8
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