Download MendeleyCrystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima
Yoshikawa, S., Nakagawa, N., Shirouzu, M., Yokoyama, S., Kuramitsu, S.To be published.
3HJN
Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima
- PDB DOI: https://doi.org/10.2210/pdb3HJN/pdb
- Entry: 3HJN supersedes: 2Z0H
- Classification: TRANSFERASE
- Organism(s): Thermotoga maritima MSB8
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-05-22 Released: 2009-06-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.285
- R-Value Work: 0.226
Starting Model: experimental
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This is version 1.2 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 |
| Thymidylate kinase | 197 | Thermotoga maritima MSB8 | Mutation(s): 0 Gene Names: tmk, TM_1099 EC: 2.7.4.9 |  | |
UniProt | |||||
Find proteins for Q9X0I3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0I3 Go to UniProtKB: Q9X0I3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9X0I3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADP Query on ADP | C [auth A], F [auth B] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N |  | ||
| TYD Query on TYD | D [auth A], G [auth B] | THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N |  | ||
| MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.285
- R-Value Work: 0.226
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.587 | α = 90 |
| b = 127.05 | β = 90 |
| c = 133.519 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| MOLREP | phasing |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2009-06-02 Deposition Author(s): Yoshikawa, S., Nakagawa, N., Shirouzu, M., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
- This entry supersedes: 2Z0H
Revision History (Full details and data files)
- Version 1.0: 2009-06-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
