MolNFT v1 · #141928 · protein
Crystal structure of aprt from Y. pseudotuberculosis with bound adenine (P21 space group).
5ZNQ · Adenine phosphoribosyltransferase: “Crystal structure of aprt from Y. pseudotuberculosis with bound adenine (P21 space group).”. X-ray diffraction, 3 ligands (ADE, NA, CL), 3 pockets (best druggability 0.68). MolNFT v1 #141928 on…
- PDB
- 5ZNQ
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- Q66DQ2
- Ligands
- ADE, NA, CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 183 | 37% helix, 33% strand | Q66DQ2 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.68 | 0.78 | 45 | ADE, CL |
| 2 | 506 | 0.66 | 0.77 | 38 | ADE, CL |
| 3 | 66 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1441 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5ZNQ · Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P21 space group). · the same entry in another collection · chain A against A, TM-score 1.00
- Q66DQ2 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase (Q66DQ2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q66DQ2
- Elsewhere: RCSB PDB 5ZNQ · PDBe 5ZNQ · UniProt Q66DQ2
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