Download MendeleyCrystal Structure of Nucleoside Kinase from Chlorobium tepidum in Complex with AMP
Satyanarayana, L., Burley, S.K., Swaminathan, S.To be published.
3KD6
Crystal Structure of Nucleoside Kinase from Chlorobium tepidum in Complex with AMP
- PDB DOI: https://doi.org/10.2210/pdb3KD6/pdb
- Classification: TRANSFERASE
- Organism(s): Chlorobaculum tepidum
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-10-22 Released: 2009-11-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 Å
- R-Value Free: 0.237
- R-Value Work: 0.212
- R-Value Observed: 0.212
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 |
| Carbohydrate kinase, PfkB family | 313 | Chlorobaculum tepidum | Mutation(s): 0 Gene Names: CT0976 |  | |
UniProt | |||||
Find proteins for Q8KDR9 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KDR9 Go to UniProtKB: Q8KDR9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8KDR9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AMP Query on AMP | C [auth A], E [auth B] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |  | ||
| GOL Query on GOL | D [auth A], F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| 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: 1.88 Å
- R-Value Free: 0.237
- R-Value Work: 0.212
- R-Value Observed: 0.212
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.014 | α = 90 |
| b = 89.797 | β = 92.9 |
| c = 64.827 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| SHELXCD | phasing |
| SHARP | phasing |
| CNS | refinement |
| DENZO | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-11-03 Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2009-11-03
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
