MolNFT v1 · #154760 · protein
Crystal structure of the pseudomonas aeruginosa dihydropyrimidinase complexed with 5-fu
6KLK · D-HYDANTOINASE/DIHYDROPYRIMIDINASE: “Crystal structure of the pseudomonas aeruginosa dihydropyrimidinase complexed with 5-fu”. X-ray diffraction, 2 ligands (URF, ZN), 5 pockets (best druggability 0.67). MolNFT v1 #154760 on…
- PDB
- 6KLK
- Type
- protein
- Length
- 956 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-HYDANTOINASE/DIHYDROPYRIMIDINASE
- EC
- 3.5.2.2
- UniProt
- Q9I676
- Ligands
- URF, ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-HYDANTOINASE/DIHYDROPYRIMIDINASE (EC 3.5.2.2) | protein | 478 | 36% helix, 23% strand | Q9I676 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.67 | 0.77 | 46 | empty |
| 2 | 450 | 0.65 | 0.78 | 42 | empty |
| 3 | 172 | 0.49 | 0.77 | 32 | empty |
| 4 | 134 | 0.48 | 0.79 | 28 | empty |
| 5 | 161 | 0.47 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1901 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 6KLK · Crystal structure of the Pseudomonas aeruginosa dihydropyrimidinase complexed with 5-FU · 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 6KLK · PDBe 6KLK · UniProt Q9I676
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