Research workbench
Crystal structure of orotidine monophosphate decarboxylase complex with xmp
Analyse Crystal structure of orotidine monophosphate decarboxylase complex with xmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LOL
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-monophosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- O26232
- Ligands
- XMP
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23) | protein | 204 | 49% helix, 20% strand | O26232 |
| B | Orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23) | protein | 214 | 51% helix, 18% strand | O26232 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
- BU2 · 1,3-butanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.66 | 0.81 | 39 | BU2, XMP |
| 2 | 245 | 0.65 | 0.83 | 34 | BU2, XMP |
| 3 | 56 | 0.35 | 0.78 | 14 | empty |
| 4 | 52 | 0.34 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1613 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1LOL · Crystal structure of orotidine monophosphate decarboxylase complex with XMP · 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 1LOL · PDBe 1LOL · UniProt O26232
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