Download MendeleyX-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and methylmalonate
Kanazawa, H., Tsunoda, M., Hoque, M.M., Suzuki, K., Yamamoto, T., Takenaka, A.To be published.
3W8D
Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate
- PDB DOI: https://doi.org/10.2210/pdb3W8D/pdb
- Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
- Organism(s): Alcaligenes faecalis
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-03-12 Released: 2014-03-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.37 Å
- R-Value Free: 0.184
- R-Value Work: 0.155
- R-Value Observed: 0.158
This is version 1.1 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-3-hydroxybutyrate dehydrogenase | 260 | Alcaligenes faecalis | Mutation(s): 0 EC: 1.1.1.30 |  | |
UniProt | |||||
Find proteins for D0VWQ0 (Alcaligenes faecalis) Explore D0VWQ0 Go to UniProtKB: D0VWQ0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0VWQ0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD Query on NAD | B [auth A] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N |  | ||
| DXX Query on DXX | C [auth A] | METHYLMALONIC ACID C4 H6 O4 ZIYVHBGGAOATLY-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | E [auth A], F [auth A], G [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.37 Å
- R-Value Free: 0.184
- R-Value Work: 0.155
- R-Value Observed: 0.158
- Space Group: P 42 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 62.74 | α = 90 |
| b = 62.74 | β = 90 |
| c = 119.22 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
Entry History
Deposition Data
- Released Date: 2014-03-12 Deposition Author(s): Kanazawa, H., Tsunoda, M., Hoque, M.M., Suzuki, K., Yamamoto, T., Takenaka, A.
Revision History (Full details and data files)
- Version 1.0: 2014-03-12
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
