Research workbench
Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus horikoshii OT3 complexed with ump
Analyse Crystal structure of orotidine 5'-phosphate decarboxylase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CZE
- Type
- protein
- Length
- 416 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
- O58462
- Ligands
- U5P
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 208 | 50% helix, 18% strand | O58462 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A
- GOL · Glycerol · additive · chains A
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 | 104 | 0.76 | 0.96 | 28 | U5P |
| 2 | 99 | 0.75 | 0.96 | 28 | U5P |
Interfaces
1 interface between chains.
- A–B · 1829 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2CZE · Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3… · the same entry in another collection · chain A against A, TM-score 1.00
- O58462 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (O58462) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O58462
- Elsewhere: RCSB PDB 2CZE · PDBe 2CZE · UniProt O58462
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