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Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1
Analyse Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E5C
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
- Molecule
- D-hydantoinase/dihydropyrimidinase
- EC
- 3.5.2.2
- UniProt
- Q9I676
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-hydantoinase/dihydropyrimidinase (EC 3.5.2.2) | protein | 478 | 36% helix, 23% strand | Q9I676 |
| C | D-hydantoinase/dihydropyrimidinase (EC 3.5.2.2) | protein | 479 | 36% helix, 23% strand | Q9I676 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.65 | 0.77 | 46 | empty |
| 2 | 504 | 0.64 | 0.76 | 47 | empty |
| 3 | 178 | 0.51 | 0.78 | 36 | empty |
| 4 | 153 | 0.47 | 0.76 | 28 | empty |
| 5 | 114 | 0.44 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 1893 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 5E5C · Crystal structure of dihydropyrimidinase from pseudomonas aeruginosa PAO1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I676 · AlphaFold monomer V2.0 prediction for D-HYDANTOINASE/DIHYDROPYRIMIDINASE (Q9I676) · a predicted model of the same protein · 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 Q9I676
- Elsewhere: RCSB PDB 5E5C · PDBe 5E5C · UniProt Q9I676
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