MolNFT v1 · #79267 · protein
Crystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from methanobacterium thermoautotrophicum complexed with the inhibitor 6AZAUMP
3SY5 · Orotidine 5'-phosphate decarboxylase: “Crystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from methanobacterium…”. X-ray diffraction, 1 ligand (UP6), 2 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 3SY5
- 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
- Pockets
- 2 · best druggability 0.79
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 | 51% helix, 19% strand | O26232 |
Ligands and binding sites
- UP6 · 6-aza uridine 5'-monophosphate · ligand · 2 copies · chains A, B
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 | 129 | 0.79 | 0.97 | 34 | UP6 |
| 2 | 124 | 0.75 | 0.94 | 29 | UP6 |
Interfaces
1 interface between chains.
- A–B · 1756 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3SY5 · Crystal structure of the mutant S127A of orotidine 5'-monophosphate decarboxylase from… · 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 3SY5 · PDBe 3SY5 · UniProt O26232
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