Download MendeleyCrystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis
Pavithra, G.C., Ramagopal, U.A.To be published.
5ZC7
Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 space group).
- PDB DOI: https://doi.org/10.2210/pdb5ZC7/pdb
- Classification: TRANSFERASE
- Organism(s): Yersinia pseudotuberculosis IP 32953
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-02-15 Released: 2019-02-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.192
- R-Value Work: 0.160
- R-Value Observed: 0.162
This is version 1.1 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 | 187 | Yersinia pseudotuberculosis IP 32953 | Mutation(s): 0 Gene Names: apt, YPTB0991 EC: 2.4.2.7 |  | |
UniProt | |||||
Find proteins for Q66DQ2 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66DQ2 Go to UniProtKB: Q66DQ2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q66DQ2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADE (Subject of Investigation/LOI) Query on ADE | D [auth A], I [auth B] | ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | H [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NI (Subject of Investigation/LOI) Query on NI | C [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A], G [auth A], K [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | E [auth A], J [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.192
- R-Value Work: 0.160
- R-Value Observed: 0.162
- Space Group: P 63
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 121.074 | α = 90 |
| b = 121.074 | β = 90 |
| c = 50.035 | γ = 120 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2019-02-20 Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.
Revision History (Full details and data files)
- Version 1.0: 2019-02-20
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
