Research workbench
Crystal structure of the mutant D70G of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 5-fluorouridine 5'-monophosphate
Analyse Crystal structure of the mutant D70G of orotidine 5'-monophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G1V
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- O26232
- Ligands
- 5FU, CL
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 213 | 50% helix, 19% strand | O26232 |
Ligands and binding sites
- 5FU · 5-fluoro-uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.80 | 0.96 | 34 | 5FU, CL |
| 2 | 145 | 0.79 | 0.96 | 32 | 5FU, CL |
Interfaces
1 interface between chains.
- A–B · 1702 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3G1V · Crystal structure of the mutant D70G of orotidine 5'-monophosphate decarboxylase from… · 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 O26232
- Elsewhere: RCSB PDB 3G1V · PDBe 3G1V · UniProt O26232
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