Download MendeleyCrystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.
Lipowska, J., Shabalin, I.G., Almo, S.C., Minor, W.To be published.
5VG6
Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.
- PDB DOI: https://doi.org/10.2210/pdb5VG6/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Xanthobacter autotrophicus Py2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-04-10 Released: 2017-04-26
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.233
- R-Value Work: 0.200
- R-Value Observed: 0.201
Starting Model: experimental
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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 |
| D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding | 341 | Xanthobacter autotrophicus Py2 | Mutation(s): 0 Gene Names: Xaut_2571 |  | |
UniProt | |||||
Find proteins for A7IIH0 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7IIH0 Go to UniProtKB: A7IIH0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A7IIH0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NDP Query on NDP | BA [auth J] K [auth A] N [auth B] P [auth C] R [auth D] | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N |  | ||
| MES Query on MES | AA [auth I] CA [auth J] L [auth A] M [auth A] O [auth B] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.233
- R-Value Work: 0.200
- R-Value Observed: 0.201
- Space Group: P 21 21 2
- Diffraction Data: https://doi.org/10.18430/M35VG6
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 132.514 | α = 90 |
| b = 311.036 | β = 90 |
| c = 98.977 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-04-26 Deposition Author(s): Lipowska, J., Shabalin, I.G., Kutner, J., Gasiorowska, O.A., 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 | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-04-26
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Refinement description - Version 1.2: 2020-01-01
Changes: Author supporting evidence - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
