Research workbench
Crystal structure of orotidine 5'-phosphate decarboxylase complexed to 6-hydroxyuridine 5'-phosphate (bmp)
Analyse Crystal structure of orotidine 5'-phosphate decarboxylase complexed to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DQX
- Type
- protein
- Length
- 1,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- P03962
- Ligands
- BMP
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 267 | 44% helix, 15% strand | P03962 |
Ligands and binding sites
- BMP · 6-hydroxyuridine-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.97 | 31 | BMP |
| 2 | 118 | 0.78 | 0.97 | 29 | BMP |
| 3 | 123 | 0.78 | 0.96 | 32 | BMP |
| 4 | 162 | 0.75 | 0.92 | 37 | BMP |
Interfaces
2 interfaces between chains.
- C–D · 1957 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1946 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1DQX · Crystal structure of orotidine 5'-phosphate decarboxylase complexed to 6-hydroxyuridine… · the same entry in another collection · chain A against A, TM-score 1.00
- P03962 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (P03962) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P03962
- Elsewhere: RCSB PDB 1DQX · PDBe 1DQX · UniProt P03962
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.