Research workbench
Crystal structure of orotidine 5'-monophosphate decarboxylase from thermoproteus neutrophilus complexed with inhibitor bmp
Analyse Crystal structure of orotidine 5'-monophosphate decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DF1
- Type
- protein
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- UniProt
- B1Y9Q9
- Ligands
- BMP, NI
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase | protein | 199 | 40% helix, 23% strand | B1Y9Q9 |
Ligands and binding sites
- BMP · 6-hydroxyuridine-5'-phosphate · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 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 | 106 | 0.76 | 0.96 | 25 | BMP |
| 2 | 117 | 0.76 | 0.95 | 30 | BMP |
Interfaces
1 interface between chains.
- A–B · 1749 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DF1 · Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus… · 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 B1Y9Q9
- Elsewhere: RCSB PDB 4DF1 · PDBe 4DF1 · UniProt B1Y9Q9
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