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Crystal structure of ADP-ATP complex of purk: N5-carboxyaminoimidazole ribonucleotide synthetase
Analyse Crystal structure of ADP-ATP 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
- 3V4S
- Type
- protein
- Length
- 761 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
- C3PBM5
- Ligands
- ADP, ATP, MG, CO3
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylaminoimidazole carboxylase, ATPase subunit (EC 4.1.1.21) | protein | 380 | 36% helix, 26% strand | C3PBM5 |
| B | Phosphoribosylaminoimidazole carboxylase, ATPase subunit (EC 4.1.1.21) | protein | 381 | 36% helix, 26% strand | C3PBM5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · 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 | 370 | 0.86 | 0.95 | 40 | empty |
| 2 | 810 | 0.77 | 0.81 | 72 | ATP, MG, CO3 |
| 3 | 814 | 0.75 | 0.79 | 75 | ADP, MG, CO3 |
| 4 | 101 | 0.40 | 0.77 | 20 | empty |
| 5 | 84 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1686 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3V4S · Crystal Structure of ADP-ATP 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 C3PBM5
- Elsewhere: RCSB PDB 3V4S · PDBe 3V4S · UniProt C3PBM5
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