Download MendeleyCrystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.To be published.
2PBR | pdb_00002pbr
Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5
- PDB DOI: https://doi.org/10.2210/pdb2PBR/pdb
- Classification: TRANSFERASE
- Organism(s): Aquifex aeolicus VF5
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-03-29 Released: 2007-10-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.96 Å
- R-Value Free: 0.242 (Depositor), 0.240 (DCC)
- R-Value Work: 0.194 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.194 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
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 | 195 | Aquifex aeolicus VF5 | Mutation(s): 0 EC: 2.7.4.9 |  | |
UniProt | |||||
Find proteins for O67099 (Aquifex aeolicus (strain VF5)) Explore O67099 Go to UniProtKB: O67099 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O67099 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], D [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.96 Å
- R-Value Free: 0.242 (Depositor), 0.240 (DCC)
- R-Value Work: 0.194 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.194 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 42.765 | α = 95.19 |
| b = 50.478 | β = 90.81 |
| c = 52.823 | γ = 111.68 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-10-02 Deposition Author(s): Jeyakanthan, J., Kanaujia, S.P., Vasuki Ranjani, C., 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: 2007-10-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance - Version 1.2: 2023-10-25
Changes: Data collection, Database references, Refinement description
