Research workbench
Crystal structure of human aprt-TYR105PHE variant in complex with adenine, prpp and MG2+, 14 hours post crystallization
Analyse Crystal structure of human aprt-TYR105PHE variant in complex with adenine, prpp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FD4
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- P07741
- Ligands
- PRP, MG
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 176 | 36% helix, 35% strand | P07741 |
| A | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 178 | 35% helix, 35% strand | P07741 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.72 | 0.79 | 69 | MG, PRP |
| 2 | 98 | 0.39 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1584 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6FD4 · Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+… · the same entry in another collection · chain B against B, 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 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 P07741
- Elsewhere: RCSB PDB 6FD4 · PDBe 6FD4 · UniProt P07741
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