4KCT
Pyruvate kinase (PYK) from Trypanosoma brucei soaked with Oxaloacetate
- PDB DOI: https://doi.org/10.2210/pdb4KCT/pdb
- Classification: TRANSFERASE
- Organism(s): Trypanosoma brucei brucei
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-04-24 Released: 2014-01-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.183
- R-Value Work: 0.153
- R-Value Observed: 0.154
This is version 2.0 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Pyruvate kinase 1 | A [auth B], B [auth A] | 499 | Trypanosoma brucei brucei | Mutation(s): 0 Gene Names: PYK1 EC: 2.7.1.40 |  |
UniProt | |||||
Find proteins for P30615 (Trypanosoma brucei brucei) Explore P30615 Go to UniProtKB: P30615 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P30615 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FDP Query on FDP | F [auth B], K [auth A] | 2,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 YXWOAJXNVLXPMU-ZXXMMSQZSA-N |  | ||
| GOL Query on GOL | G [auth B], L [auth A], M [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| PYR Query on PYR | E [auth B], J [auth A] | PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N |  | ||
| K Query on K | D [auth B], I [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth B], H [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.183
- R-Value Work: 0.153
- R-Value Observed: 0.154
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 102.99 | α = 90 |
| b = 108.17 | β = 90 |
| c = 264.49 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DNA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2014-01-08 Deposition Author(s): Zhong, W., Morgan, H.P., McNae, I.W., Michels, P.A.M., Fothergill-Gilmore, L.A., Walkinshaw, M.D.
Revision History (Full details and data files)
- Version 1.0: 2014-01-08
Type: Initial release - Version 1.1: 2014-02-26
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
