Download MendeleyCrystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori
Satyanarayana, L., Burley, S.K., Swaminathan, S.To be published.
3K5W
Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori
- PDB DOI: https://doi.org/10.2210/pdb3K5W/pdb
- Classification: TRANSFERASE
- Organism(s): Helicobacter pylori
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-10-08 Released: 2009-12-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.262
- R-Value Work: 0.233
- R-Value Observed: 0.233
wwPDB Validation 3D Report Full Report
This is version 1.3 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 | 475 | Helicobacter pylori | Mutation(s): 0 Gene Names: 900323 |  | |
UniProt | |||||
Find proteins for P56176 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56176 Go to UniProtKB: P56176 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P56176 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | B [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| 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: 2.60 Å
- R-Value Free: 0.262
- R-Value Work: 0.233
- R-Value Observed: 0.233
- Space Group: I 4 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 119.955 | α = 90 |
| b = 119.955 | β = 90 |
| c = 162.226 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CBASS | data collection |
| SHELXS | phasing |
| CNS | refinement |
| DENZO | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-12-08 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: 2009-12-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2019-11-13
Changes: Derived calculations, Structure summary - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
