Download MendeleyCrystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8
Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H.To be published.
1UB0
Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8
- PDB DOI: https://doi.org/10.2210/pdb1UB0/pdb
- Classification: TRANSFERASE
- Organism(s): Thermus thermophilus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2003-03-26 Released: 2003-04-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.232
- R-Value Work: 0.207
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Phosphomethylpyrimidine Kinase | 258 | Thermus thermophilus | Mutation(s): 0 Gene Names: ThiD EC: 2.7.4.7 (PDB Primary Data), 2.7.1.49 (UniProt) |  | |
UniProt | |||||
Find proteins for Q7SIA0 (Thermus thermophilus) Explore Q7SIA0 Go to UniProtKB: Q7SIA0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7SIA0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | E [auth A], F [auth A], G [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| DIO Query on DIO | C [auth A], D [auth A] | 1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.232
- R-Value Work: 0.207
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 105.145 | α = 90 |
| b = 105.145 | β = 90 |
| c = 105.469 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| SCALEPACK | data scaling |
| CNS | refinement |
| HKL-2000 | data reduction |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2003-04-08 Deposition Author(s): Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2003-04-08
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
