MolNFT v1 · #148664 · protein
Crystal structure of human aprt-TYR105PHE variant in complex with adenine, prpp and MG2+, 30 days post crystallization (with AMP and ppi products fully generated)
6FD6 · Adenine phosphoribosyltransferase: “Crystal structure of human aprt-TYR105PHE variant in complex with adenine, prpp and MG2+, 30 days post…”. X-ray diffraction, 3 ligands (AMP, PPV, MG), 2 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6FD6
- Type
- protein
- Length
- 356 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
- AMP, PPV, MG
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 178 | 35% helix, 35% strand | P07741 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
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 | 820 | 0.75 | 0.79 | 67 | AMP, PPV, MG |
| 2 | 106 | 0.41 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1550 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6FD6 · Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+… · the same entry in another collection · chain A against A, TM-score 1.00
- P07741 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase (P07741) · a predicted model of the same protein · chain A 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 6FD6 · PDBe 6FD6 · UniProt P07741
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