Download MendeleyProbable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L-tartaric acid
Langner, K.M., Shabalin, I.G., Handing, K.B., Gasiorowska, O.A., Chowdhury, S., Zimmerman, M.D., Minor, W.To be published.
5BQF
Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid
- PDB DOI: https://doi.org/10.2210/pdb5BQF/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Rhizobium etli CFN 42
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-05-29 Released: 2015-06-17
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.165
- R-Value Work: 0.139
- R-Value Observed: 0.140
This is version 1.4 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 |
| NADP-dependent 2-hydroxyacid dehydrogenase | 322 | Rhizobium etli CFN 42 | Mutation(s): 0 Gene Names: RHE_CH00179 |  | |
UniProt | |||||
Find proteins for Q2KDT2 (Rhizobium etli (strain CFN 42 / ATCC 51251)) Explore Q2KDT2 Go to UniProtKB: Q2KDT2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2KDT2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAP Query on NAP | D [auth A] | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N |  | ||
| EPE Query on EPE | B [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| TLA Query on TLA | E [auth A] | L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N |  | ||
| PEG Query on PEG | C [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| CL Query on CL | G [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | F [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.165
- R-Value Work: 0.139
- R-Value Observed: 0.140
- Space Group: P 41 21 2
- Diffraction Data: https://doi.org/10.18430/M3T885
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.692 | α = 90 |
| b = 65.692 | β = 90 |
| c = 151.406 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-3000 | phasing |
| Coot | model building |
| MOLREP | phasing |
| HKL-3000 | data scaling |
| HKL-3000 | data reduction |
| HKL-3000 | data collection |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-06-17 Deposition Author(s): Langner, K.M., Shabalin, I.G., Handing, K.B., Gasiorowska, O.A., Stead, M., Hillerich, B.S., Chowdhury, S., Hammonds, J., Zimmerman, M.D., Al Obaidi, N., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | U54-GM094662 |
Revision History (Full details and data files)
- Version 1.0: 2015-06-17
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy - Version 1.2: 2020-01-01
Changes: Author supporting evidence - Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary - Version 1.4: 2023-09-27
Changes: Data collection, Refinement description
