MolNFT v1 · #80248 · protein
Structure of a orotidine 5'-phosphate decarboxylase (pyrf) from coxiella burnetii
3TR2: “Structure of a orotidine 5'-phosphate decarboxylase (pyrf) from coxiella burnetii”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #80248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3TR2
- Type
- protein
- Length
- 440 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
- Q83E06
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 219 | 47% helix, 18% strand | Q83E06 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 221 | 48% helix, 17% strand | Q83E06 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.69 | 0.95 | 23 | empty |
| 2 | 430 | 0.67 | 0.80 | 41 | empty |
| 3 | 364 | 0.65 | 0.80 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 1738 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3TR2 · Structure of a orotidine 5'-phosphate decarboxylase (pyrF) from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
- Q83E06 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q83E06) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q83E06
- Elsewhere: RCSB PDB 3TR2 · PDBe 3TR2 · UniProt Q83E06
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