Research workbench
Crystal structure of the orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate
Analyse Crystal structure of the 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
- 3GDL
- Type
- protein
- Length
- 514 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
- P03962
- Ligands
- UP6
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 257 | 47% helix, 16% strand | P03962 |
Ligands and binding sites
- UP6 · 6-aza uridine 5'-monophosphate · 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 | 148 | 0.75 | 0.93 | 36 | UP6 |
| 2 | 155 | 0.74 | 0.92 | 37 | UP6 |
| 3 | 54 | 0.30 | 0.76 | 16 | empty |
| 4 | 51 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1901 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3GDL · Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces… · the same entry in another collection · chain A against A, TM-score 1.00
- P03962 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (P03962) · 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 P03962
- Elsewhere: RCSB PDB 3GDL · PDBe 3GDL · UniProt P03962
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