MolNFT v1 · #101758 · protein
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-hydroxyuridine 5'-monophosphate
4O11 · Orotidine 5'-phosphate decarboxylase: “Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum…”. X-ray diffraction, 3 ligands (BMP, MG, CL), 2 pockets (best druggability 0.78). MolNFT…
- PDB
- 4O11
- Type
- protein
- Length
- 440 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
- BMP, MG, CL
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 220 | 49% helix, 19% strand | O26232 |
Ligands and binding sites
- BMP · 6-hydroxyuridine-5'-phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · 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 | 125 | 0.78 | 0.96 | 34 | BMP |
| 2 | 126 | 0.74 | 0.93 | 28 | BMP |
Interfaces
1 interface between chains.
- A–B · 1760 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4O11 · Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium… · 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 4O11 · PDBe 4O11 · UniProt O26232
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.