Research workbench
Crystal structure of the mutant V182A.R203A of orotidine 5'- monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with inhibitor bmp
Analyse Crystal structure of the mutant V182A.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
- 4FX6
- Type
- protein
- Length
- 444 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
- BMP
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 218 | 50% helix, 19% strand | O26232 |
| N | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 226 | 48% helix, 18% strand | O26232 |
Ligands and binding sites
- BMP · 6-hydroxyuridine-5'-phosphate · ligand · 2 copies · chains M, N
- GOL · Glycerol · additive · 4 copies · chains M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.77 | 0.91 | 48 | BMP, GOL |
| 2 | 165 | 0.71 | 0.89 | 28 | BMP |
| 3 | 64 | 0.38 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- M–N · 1617 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4FX6 · Crystal structure of the mutant V182A.R203A of orotidine 5'-monophosphate decarboxylase… · the same entry in another collection · chain M against M, 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 4FX6 · PDBe 4FX6 · UniProt O26232
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