Research workbench
Crystal structure of orotidine monophosphate decarboxylase complexed with 6-azaump
Analyse Crystal structure of orotidine monophosphate decarboxylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DVJ
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- 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
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 239 | 53% helix, 17% strand | O26232 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 211 | 52% helix, 19% strand | O26232 |
| C | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 236 | 52% helix, 17% strand | O26232 |
| D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 214 | 50% helix, 19% strand | O26232 |
Ligands and binding sites
- UP6 · 6-aza uridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.57 | 0.80 | 27 | UP6 |
| 2 | 184 | 0.56 | 0.80 | 29 | UP6 |
| 3 | 193 | 0.56 | 0.80 | 28 | UP6 |
| 4 | 167 | 0.55 | 0.80 | 29 | UP6 |
| 5 | 137 | 0.45 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1DVJ · Crystal structure of orotidine monophosphate decarboxylase complexed with 6-azaump · 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 1DVJ · PDBe 1DVJ · UniProt O26232
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.