Research workbench
Crystal structure of ADP complex of purk: N5-carboxyaminoimidazole ribonucleotide synthetase
Analyse Crystal structure of ADP 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
- 3QFF
- Type
- protein
- Length
- 754 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N5-carboxyaminoimidazole ribonucleotide synthetase
- EC
- 4.1.1.21
- UniProt
- C3PBM5
- Ligands
- ADP
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N5-carboxyaminoimidazole ribonucleotide synthetase (EC 4.1.1.21) | protein | 377 | 35% helix, 27% strand | C3PBM5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 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 | 354 | 0.86 | 0.96 | 40 | empty |
| 2 | 876 | 0.77 | 0.80 | 63 | ADP |
| 3 | 783 | 0.75 | 0.80 | 63 | ADP |
| 4 | 106 | 0.43 | 0.78 | 19 | empty |
| 5 | 96 | 0.41 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1645 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3QFF · Crystal Structure of ADP 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 3QFF · PDBe 3QFF · UniProt C3PBM5
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