Download MendeleyCrystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima
Ramagopal, U.A., Toro, R., Freeman, J., Chang, S., Maletic, M., Gheyi, T., Burley, S.K., Almo, S.C.To be published.
3EZY
Crystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima
- PDB DOI: https://doi.org/10.2210/pdb3EZY/pdb
- Classification: structural genomics, unknown function
- Organism(s): Thermotoga maritima
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-10-24 Released: 2009-01-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.04 Å
- R-Value Free: 0.223
- R-Value Work: 0.175
- R-Value Observed: 0.177
wwPDB Validation 3D Report Full Report
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 |
| Dehydrogenase | 344 | Thermotoga maritima | Mutation(s): 0 Gene Names: TM_0414 |  | |
UniProt | |||||
Find proteins for Q9WYP5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYP5 Go to UniProtKB: Q9WYP5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9WYP5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | G [auth C], H [auth C] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| MRD Query on MRD | E [auth A], F [auth B], I [auth D] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.04 Å
- R-Value Free: 0.223
- R-Value Work: 0.175
- R-Value Observed: 0.177
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 69.144 | α = 90 |
| b = 108.739 | β = 96.26 |
| c = 98.496 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| HKL-2000 | data reduction |
| HKL2Map | phasing |
Entry History
Deposition Data
- Released Date: 2009-01-13 Deposition Author(s): Ramagopal, U.A., Toro, R., Freeman, J., Chang, S., Maletic, M., Gheyi, T., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2009-01-13
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.4: 2023-12-27
Changes: Data collection, Database references
