MolNFT v1 · #141581 · protein
Crystal structure of aprt from Y. pseudotuberculosis with bound adenine (P63 space group).
5ZC7 · Adenine phosphoribosyltransferase: “Crystal structure of aprt from Y. pseudotuberculosis with bound adenine (P63 space group).”. X-ray diffraction, 4 ligands (ADE, NA, NI), 2 pockets (best druggability 0.67). MolNFT v1 #141581 on…
- PDB
- 5ZC7
- Type
- protein
- Length
- 363 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, NI, CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 182 | 36% helix, 32% strand | Q66DQ2 |
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 181 | 36% 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
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.67 | 0.78 | 38 | ADE, CL |
| 2 | 437 | 0.64 | 0.77 | 40 | ADE, CL |
Interfaces
1 interface between chains.
- A–B · 1499 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5ZC7 · Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 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 A against A, TM-score 0.99
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 5ZC7 · PDBe 5ZC7 · UniProt Q66DQ2
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