Download MendeleyCrystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7
Kanaujia, S.P., Jeyakanthan, J., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.To be published.
2PLR
Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7
- PDB DOI: 10.2210/pdb2PLR/pdb
- Classification: TRANSFERASE
- Organism(s): Sulfurisphaera tokodaii str. 7
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-04-20 Released: 2008-04-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.209
- R-Value Work: 0.185
- R-Value Observed: 0.185
wwPDB Validation 3D Report Full Report
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 |
| Probable thymidylate kinase | A, B | 213 | Sulfurisphaera tokodaii str. 7 | Mutation(s): 0 Gene Names: tmk, STK_15430 EC: 2.7.4.9 |  |
UniProt | |||||
Find proteins for Q970Q8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970Q8 Go to UniProtKB: Q970Q8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q970Q8 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 9 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | N [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | Ligand Interaction | |
| 1PE Query on 1PE | F [auth A], V [auth B], W [auth B] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | Ligand Interaction | |
| PG4 Query on PG4 | AA [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | Ligand Interaction | |
| DTT Query on DTT | M [auth A] | 2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N |  | Ligand Interaction | |
| PGE Query on PGE | G [auth A], H [auth A], I [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | Ligand Interaction | |
| PEG Query on PEG | BA [auth B], CA [auth B], DA [auth B], EA [auth B], O [auth A], | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | Ligand Interaction | |
| PO4 Query on PO4 | E [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | Ligand Interaction | |
| EDO Query on EDO | J [auth A], K [auth A], L [auth A], X [auth B], Y [auth B], | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | C [auth A], D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.209
- R-Value Work: 0.185
- R-Value Observed: 0.185
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.523 | α = 90 |
| b = 62.873 | β = 90 |
| c = 137.332 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2008-04-22 Deposition Author(s): Kanaujia, S.P., Jeyakanthan, J., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2008-04-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
