Research workbench
Crystal structure of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with 6-azauridine 5'- monophosphate
Analyse Crystal structure of 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
- 4NX5
- Type
- protein
- Length
- 439 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
- UP6, MG, CL
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 220 | 49% helix, 19% strand | O26232 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 219 | 52% helix, 19% strand | O26232 |
Ligands and binding sites
- UP6 · 6-aza uridine 5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
- EDO · 1,2-ethanediol · 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 | 116 | 0.78 | 0.97 | 33 | UP6 |
| 2 | 123 | 0.78 | 0.96 | 33 | UP6 |
Interfaces
1 interface between chains.
- A–B · 1758 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4NX5 · 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 4NX5 · PDBe 4NX5 · UniProt O26232
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.