Research workbench
Crystal structure of orotidine 5'-phosphate decarboxylase from lactobacillus acidophilus
Analyse Crystal structure of orotidine 5'-phosphate decarboxylase from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TFX
- Type
- protein
- Length
- 455 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
- Q5FJB3
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 231 | 48% helix, 16% strand | Q5FJB3 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 224 | 47% helix, 17% strand | Q5FJB3 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.64 | 0.80 | 40 | empty |
| 2 | 366 | 0.63 | 0.78 | 47 | empty |
| 3 | 51 | 0.25 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1922 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3TFX · Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5FJB3 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q5FJB3) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q5FJB3
- Elsewhere: RCSB PDB 3TFX · PDBe 3TFX · UniProt Q5FJB3
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