Research workbench
The crystal structure of di-zn dihydropyrimidinase in complex with ncbi
Analyse The crystal structure of di-zn dihydropyrimidinase in complex with ncbi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LCQ
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase
- Ligands
- URQ, ZN
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropyrimidinase | protein | 485 | 36% helix, 23% strand | — |
Ligands and binding sites
- URQ · (2S)-3-(carbamoylamino)-2-methylpropanoic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.50 | 0.79 | 18 | empty |
| 2 | 81 | 0.37 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 4LCQ · The crystal structure of di-Zn dihydropyrimidinase in complex with NCBI · 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
- Elsewhere: RCSB PDB 4LCQ · PDBe 4LCQ
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