Research workbench
Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human ump synthase, apo form
Analyse Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QCC
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'- phosphate decarboxylase (ompdecase)
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'- phosphate decarboxylase (ompdecase) (EC 4.1.1.23) | protein | 247 | 47% helix, 17% strand | P11172 |
| B | Orotidine 5'- phosphate decarboxylase (ompdecase) (EC 4.1.1.23) | protein | 249 | 45% helix, 16% strand | P11172 |
Ligands and binding sites
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 | 436 | 0.71 | 0.82 | 42 | SO4, GOL |
| 2 | 398 | 0.71 | 0.83 | 40 | SO4, GOL |
| 3 | 60 | 0.34 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1549 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2QCC · Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP… · the same entry in another collection · chain A against A, TM-score 1.00
- P11172 · AlphaFold monomer V2.0 prediction for uridine 5'-monophosphate synthase (P11172) · 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 P11172
- Elsewhere: RCSB PDB 2QCC · PDBe 2QCC · UniProt P11172
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