Download MendeleyCrystal structure of pyridoxal kinase from Lactobacillus plantarum
Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S.To be published.
3H74
Crystal structure of pyridoxal kinase from Lactobacillus plantarum
- PDB DOI: https://doi.org/10.2210/pdb3H74/pdb
- Classification: TRANSFERASE
- Organism(s): Lactiplantibacillus plantarum
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-04-24 Released: 2009-05-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.202
- R-Value Work: 0.194
- R-Value Observed: 0.194
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 |
| Pyridoxal kinase | 282 | Lactiplantibacillus plantarum | Mutation(s): 0 Gene Names: pdx, lp_0863 EC: 2.7.1.35 |  | |
UniProt | |||||
Find proteins for F9UM74 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UM74 Go to UniProtKB: F9UM74 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | F9UM74 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | B [auth A], C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.202
- R-Value Work: 0.194
- R-Value Observed: 0.194
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.005 | α = 90 |
| b = 69.649 | β = 90 |
| c = 132.15 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| SHELXS | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-05-26 Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2009-05-26
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
