MolNFT v1 · #64793 · protein
Crystal structure of the D91N mutant of the orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae complexed with 6- azauridine 5'-monophosphate
3GDT · Orotidine 5'-phosphate decarboxylase: “Crystal structure of the D91N mutant of the orotidine 5'-monophosphate decarboxylase from saccharomyces…”. X-ray diffraction, 1 ligand (UP6), 11 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 3GDT
- Type
- protein
- Length
- 1,024 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
- P03962
- Ligands
- UP6
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 260 | 49% helix, 17% strand | P03962 |
| C, D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 252 | 48% helix, 15% strand | P03962 |
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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.68 | 0.80 | 44 | UP6 |
| 2 | 233 | 0.68 | 0.85 | 34 | empty |
| 3 | 527 | 0.67 | 0.78 | 31 | empty |
| 4 | 264 | 0.58 | 0.78 | 30 | UP6 |
| 5 | 202 | 0.51 | 0.77 | 36 | UP6 |
Interfaces
5 interfaces between chains.
- A–D · 1207 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 176 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 112 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GDT · Crystal structure of the D91N mutant of the orotidine 5'-monophosphate decarboxylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P03962 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (P03962) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P03962
- Elsewhere: RCSB PDB 3GDT · PDBe 3GDT · UniProt P03962
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