Download MendeleyCrystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae
Satyanarayana, L., Burley, S.K., Swaminathan, S.To be published.
3IKH
Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae
- PDB DOI: https://doi.org/10.2210/pdb3IKH/pdb
- Classification: TRANSFERASE
- Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-08-05 Released: 2009-08-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 Å
- R-Value Free: 0.240
- R-Value Work: 0.220
- R-Value Observed: 0.220
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 | 299 | Klebsiella pneumoniae subsp. pneumoniae MGH 78578 | Mutation(s): 0 Gene Names: KPN78578_16990, KPN78578_16990/5340552, KPN_01729, rbsK EC: 2.7.1.15 |  | |
UniProt | |||||
Find proteins for A6T989 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T989 Go to UniProtKB: A6T989 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6T989 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | E [auth A], F [auth B], G [auth C], I [auth D] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | Ligand Interaction | |
| GOL Query on GOL | H [auth C], J [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | 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: 0.240
- R-Value Work: 0.220
- R-Value Observed: 0.220
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.332 | α = 90 |
| b = 106.352 | β = 99.51 |
| c = 122.056 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| MOLREP | phasing |
| CNS | refinement |
| DENZO | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-08-18 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: 2009-08-18
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
