Research workbench
Crystal structure of the mutant R203A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
Analyse Crystal structure of the mutant R203A 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
- 3LI0
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Methanothermobacter thermautotrophicus
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- O26232
- Ligands
- BMQ
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 226 | 47% helix, 18% strand | O26232 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 224 | 48% helix, 18% strand | O26232 |
Ligands and binding sites
- BMQ · 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.71 | 0.89 | 34 | BMQ |
| 2 | 162 | 0.70 | 0.89 | 31 | BMQ |
| 3 | 59 | 0.34 | 0.77 | 14 | empty |
| 4 | 62 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1684 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3LI0 · Crystal structure of the mutant R203A of orotidine 5'-monophosphate decarboxylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- O26232 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (O26232) · a predicted model of the same protein · 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 3LI0 · PDBe 3LI0 · UniProt O26232
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