MolNFT v1 · #35290 · protein
Covalent complex of orotidine 5'-monophosphate decarboxylase (odcase) with 6-iodo-ump
2E6Y · Orotidine 5'-phosphate decarboxylase: “Covalent complex of orotidine 5'-monophosphate decarboxylase (odcase) with 6-iodo-ump”. X-ray diffraction, 1 ligand (U5P), 3 pockets (best druggability 0.78). MolNFT v1 #35290 on GenesisL1: 3D…
- PDB
- 2E6Y
- Type
- protein
- Length
- 430 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
- O26232
- Ligands
- U5P
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 215 | 52% helix, 19% strand | O26232 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 116 | 0.78 | 0.97 | 40 | U5P |
| 2 | 104 | 0.75 | 0.96 | 31 | U5P |
| 3 | 52 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1698 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2E6Y · Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP · 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 O26232
- Elsewhere: RCSB PDB 2E6Y · PDBe 2E6Y · UniProt O26232
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