MolNFT v1 · #61123 · protein
Crystal structure of dihydropyrimidinase from sinorhizobium meliloti
3DC8: “Crystal structure of dihydropyrimidinase from sinorhizobium meliloti”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.83). MolNFT v1 #61123 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DC8
- Type
- protein
- Length
- 958 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase
- EC
- 3.5.2.2
- UniProt
- Q0PQZ5
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase (EC 3.5.2.2) | protein | 483 | 36% helix, 22% strand | Q0PQZ5 |
| B | Dihydropyrimidinase (EC 3.5.2.2) | protein | 475 | 37% helix, 22% strand | Q0PQZ5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.83 | 0.84 | 67 | empty |
| 2 | 111 | 0.57 | 0.85 | 23 | GOL |
| 3 | 85 | 0.57 | 0.87 | 16 | empty |
| 4 | 101 | 0.56 | 0.85 | 21 | GOL |
| 5 | 222 | 0.54 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1234 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 3DC8 · Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti · 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 Q0PQZ5
- Elsewhere: RCSB PDB 3DC8 · PDBe 3DC8 · UniProt Q0PQZ5
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