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Crystal structure of dihydropyrimidinase from saccharomyces kluyveri in complex with the reaction product N-carbamyl-beta-alanine
Analyse Crystal structure of dihydropyrimidinase from saccharomyces kluyveri in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FVM
- Type
- protein
- Length
- 2,127 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropyrimidinase
- EC
- 3.5.2.2
- UniProt
- Q9P903
- Ligands
- URP, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydropyrimidinase (EC 3.5.2.2) | protein | 532 | 33% helix, 19% strand | Q9P903 |
| C | Dihydropyrimidinase (EC 3.5.2.2) | protein | 531 | 33% helix, 19% strand | Q9P903 |
| D | Dihydropyrimidinase (EC 3.5.2.2) | protein | 532 | 33% helix, 19% strand | Q9P903 |
Ligands and binding sites
- URP · N-(aminocarbonyl)-beta-alanine · ligand · 2 copies · chains A, B
- 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.85 | 0.86 | 71 | empty |
| 2 | 1138 | 0.84 | 0.85 | 77 | empty |
| 3 | 50 | 0.72 | 0.99 | 20 | empty |
| 4 | 529 | 0.70 | 0.80 | 50 | empty |
| 5 | 329 | 0.70 | 0.83 | 47 | ZN |
Interfaces
4 interfaces between chains.
- C–D · 1963 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1956 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1186 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1182 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 2FVM · Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9P903 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase (Q9P903) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9P903
- Elsewhere: RCSB PDB 2FVM · PDBe 2FVM · UniProt Q9P903
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