Research workbench
Crystal structure E. COLI purk in complex with mg, ADP, and pi
Analyse Crystal structure E. COLI purk in complex with mg, ADP, and pi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ETJ
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylaminoimidazole carboxylase ATPase subunit
- EC
- 4.1.1.21
- UniProt
- P09029
- Ligands
- ADP, MG, PI, CL
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylaminoimidazole carboxylase ATPase subunit (EC 4.1.1.21) | protein | 355 | 36% helix, 28% strand | P09029 |
| B | Phosphoribosylaminoimidazole carboxylase ATPase subunit (EC 4.1.1.21) | protein | 351 | 34% helix, 27% strand | P09029 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PI · Hydrogenphosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.87 | 0.93 | 56 | empty |
| 2 | 459 | 0.75 | 0.84 | 53 | ADP, MG, PI |
| 3 | 516 | 0.64 | 0.76 | 49 | ADP, MG, PI |
| 4 | 61 | 0.29 | 0.74 | 16 | empty |
| 5 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1484 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3ETJ · Crystal structure E. coli Purk in complex with Mg, ADP, and Pi · the same entry in another collection · chain A against A, TM-score 1.00
- P09029 · AlphaFold monomer V2.0 prediction for N5-carboxyaminoimidazole ribonucleotide synthase… · a predicted model of the same protein · chain B 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 P09029
- Elsewhere: RCSB PDB 3ETJ · PDBe 3ETJ · UniProt P09029
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