MolNFT v1 · #140738 · protein
Crystal structure of dihydropyrimidinase from pseudomonas aeruginosa PAO1 at 2.17 ångström resolution
5YKD · D-HYDANTOINASE/DIHYDROPYRIMIDINASE: “Crystal structure of dihydropyrimidinase from pseudomonas aeruginosa PAO1 at 2.17 ångström resolution”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability 0.86). MolNFT v1 #140738 on…
- PDB
- 5YKD
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-HYDANTOINASE/DIHYDROPYRIMIDINASE
- EC
- 3.5.2.2
- UniProt
- Q9I676
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-HYDANTOINASE/DIHYDROPYRIMIDINASE (EC 3.5.2.2) | protein | 478 | 36% helix, 23% strand | Q9I676 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.86 | 0.87 | 67 | empty |
| 2 | 1200 | 0.85 | 0.86 | 64 | empty |
| 3 | 876 | 0.73 | 0.77 | 85 | empty |
| 4 | 243 | 0.61 | 0.80 | 44 | ZN |
| 5 | 254 | 0.61 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1225 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1223 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5YKD · Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17… · 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 5YKD · PDBe 5YKD · UniProt Q9I676
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.