Research workbench
Crystal structure of ATP-ca++ complex of purk: N5- carboxyaminoimidazole ribonucleotide synthetase
Analyse Crystal structure of ATP-ca++ complex of purk: N5- carboxyaminoimidazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DLK
- Type
- protein
- Length
- 760 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
- Q81ZH7
- Ligands
- ATP, CA, PO4
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoribosylaminoimidazole carboxylase, ATPase subunit (EC 4.1.1.21) | protein | 380 | 35% helix, 26% strand | Q81ZH7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
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 | 386 | 0.87 | 0.96 | 41 | empty |
| 2 | 775 | 0.76 | 0.81 | 72 | CA, ATP |
| 3 | 846 | 0.73 | 0.78 | 64 | CA, ATP |
| 4 | 96 | 0.41 | 0.77 | 21 | empty |
| 5 | 77 | 0.37 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1666 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4DLK · Crystal Structure of ATP-Ca++ complex of purK: N5-carboxyaminoimidazole ribonucleotide… · 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 Q81ZH7
- Elsewhere: RCSB PDB 4DLK · PDBe 4DLK · UniProt Q81ZH7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.