Download MendeleytRNA 2-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 5'-AMP
Jacewicz, A., Dantuluri, S., Shuman, S.To be published.
8TKB
tRNA 2-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 5'-AMP
- PDB DOI: https://doi.org/10.2210/pdb8TKB/pdb
- Classification: TRANSFERASE
- Organism(s): Pyrococcus horikoshii OT3
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2023-07-25 Released: 2024-06-19
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Other government
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.209
- R-Value Work: 0.185
- R-Value Observed: 0.186
This is version 1.0 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 |
| Probable RNA 2'-phosphotransferase | 177 | Pyrococcus horikoshii OT3 | Mutation(s): 1 Gene Names: kptA, PH0160 EC: 2.7.1 |  | |
UniProt | |||||
Find proteins for O57899 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57899 Go to UniProtKB: O57899 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O57899 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AMP (Subject of Investigation/LOI) Query on AMP | B [auth A], C [auth A] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |  | ||
| K Query on K | D [auth A], E [auth A], F [auth A], G [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
| CL Query on CL | H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | O [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.71 Å
- R-Value Free: 0.209
- R-Value Work: 0.185
- R-Value Observed: 0.186
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 38.937 | α = 90 |
| b = 43.665 | β = 90 |
| c = 122.861 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-06-19 Deposition Author(s): Jacewicz, A., Dantuluri, S., Shuman, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R35-GM126945 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P30-GM124165 |
| Department of Energy (DOE, United States) | United States | DE-AC02-06CH11357 |
| Other government | United States | HEI-S10OD021527 |
Revision History (Full details and data files)
- Version 1.0: 2024-06-19
Type: Initial release
