6FD4
Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 14 hours post crystallization
- PDB DOI: https://doi.org/10.2210/pdb6FD4/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-12-21 Released: 2018-08-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.178
- R-Value Work: 0.166
- R-Value Observed: 0.166
This is version 1.2 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Adenine phosphoribosyltransferase | A [auth B], B [auth A] | 178 | Homo sapiens | Mutation(s): 0 Gene Names: APRT EC: 2.4.2.7 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P07741 (Homo sapiens) Explore P07741 Go to UniProtKB: P07741 | |||||
PHAROS: P07741 GTEx: ENSG00000198931 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P07741 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PRP Query on PRP | D [auth B], F [auth A] | 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N |  | ||
| MG Query on MG | C [auth B], E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.178
- R-Value Work: 0.166
- R-Value Observed: 0.166
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.38 | α = 69.86 |
| b = 47.54 | β = 77.2 |
| c = 47.67 | γ = 61.76 |
| Software Name | Purpose |
|---|---|
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
Entry History
Deposition Data
- Released Date: 2018-08-15 Deposition Author(s): Nioche, P., Huyet, J., Ozeir, M.
Revision History (Full details and data files)
- Version 1.0: 2018-08-15
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary
