Research workbench
Crystal structure of human aprt wild type in complex with adenine, prpp and MG2+
Analyse Crystal structure of human aprt wild type in complex with adenine, prpp and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FCI
- Type
- protein
- Length
- 712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- P07741
- Ligands
- PRP, ADE, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 179 | 35% helix, 35% strand | P07741 |
| B, D | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 177 | 34% helix, 36% strand | P07741 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains A, D, B, C
- ADE · Adenine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 404 | 0.78 | 0.87 | 63 | MG, PRP, ADE |
| 2 | 412 | 0.78 | 0.87 | 65 | MG, PRP, ADE |
| 3 | 697 | 0.75 | 0.80 | 51 | empty |
| 4 | 83 | 0.36 | 0.76 | 16 | empty |
| 5 | 52 | 0.26 | 0.73 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1634 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1621 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FCI · Crystal Structure of Human APRT wild type in complex with Adenine, PRPP and Mg2+ · the same entry in another collection · chain D against D, TM-score 1.00
- P07741 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase (P07741) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P07741
- Elsewhere: RCSB PDB 6FCI · PDBe 6FCI · UniProt P07741
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.