MolNFT v1 · #99133 · protein
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanocaldococcus jannaschii complexed with inhibitor bmp
4LUJ · Orotidine 5'-phosphate decarboxylase: “Crystal structure of orotidine 5'-monophosphate decarboxylase from methanocaldococcus jannaschii complexed…”. X-ray diffraction, 1 ligand (BMP), 2 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 4LUJ
- Type
- protein
- Length
- 428 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
- Q57700
- Ligands
- BMP
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 214 | 49% helix, 19% strand | Q57700 |
Ligands and binding sites
- BMP · 6-hydroxyuridine-5'-phosphate · ligand · 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 | 133 | 0.79 | 0.97 | 40 | BMP |
| 2 | 140 | 0.79 | 0.96 | 42 | BMP |
Interfaces
1 interface between chains.
- A–B · 1692 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4LUJ · Crystal structure of Orotidine 5'-monophosphate decarboxylase from methanocaldococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57700 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q57700) · a predicted model of the same protein · chain A 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 Q57700
- Elsewhere: RCSB PDB 4LUJ · PDBe 4LUJ · UniProt Q57700
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