Research workbench
Crystal structure of aprt from Y. pseudotuberculosis with bound adenine (P63 space group).
Analyse Crystal structure of aprt from Y. pseudotuberculosis with bound adenine (P63… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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