Download MendeleyCrystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate
Mayclin, S.J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.To be published.
5VN4
Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate
- PDB DOI: https://doi.org/10.2210/pdb5VN4/pdb
- Classification: TRANSFERASE
- Organism(s): Trypanosoma brucei brucei TREU927
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-04-28 Released: 2017-05-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.175
- R-Value Work: 0.143
- R-Value Observed: 0.144
Starting Model: experimental
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This is version 2.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Adenine phosphoribosyltransferase, putative | 243 | Trypanosoma brucei brucei TREU927 | Mutation(s): 0 Gene Names: Tb927.7.1780 EC: 2.4.2.7 |  | |
UniProt | |||||
Find proteins for Q57V32 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q57V32 Go to UniProtKB: Q57V32 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q57V32 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HSX Query on HSX | D [auth A], H [auth B] | 5-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-AIHAYLRMSA-N |  | ||
| PPV Query on PPV | E [auth A], I [auth B] | PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N |  | ||
| ADE Query on ADE | C [auth A], G [auth B] | ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N |  | ||
| MG Query on MG | F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.175
- R-Value Work: 0.143
- R-Value Observed: 0.144
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M35VN4
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.84 | α = 90 |
| b = 72.85 | β = 90 |
| c = 85.61 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| Coot | model building |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2017-05-24 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2017-05-24
Type: Initial release - Version 1.1: 2017-06-28
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
