Download MendeleyCrystal Structure of Glycerophosphoryl Diester Phosphodiesterase complexed with Glycerol
Ishijima, J., Yutani, K.To be published.
1VD6
Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase complexed with Glycerol
- PDB DOI: 10.2210/pdb1VD6/pdb
- Classification: HYDROLASE
- Organism(s): Thermus thermophilus HB8
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2004-03-18 Released: 2005-04-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.233
- R-Value Work: 0.217
- R-Value Observed: 0.217
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Glycerophosphoryl Diester Phosphodiesterase | A | 224 | Thermus thermophilus HB8 | Mutation(s): 0 Gene Names: TTHB141 EC: 3.1.4.46 |  |
UniProt | |||||
Find proteins for Q53W25 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W25 Go to UniProtKB: Q53W25 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q53W25 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | B [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.233
- R-Value Work: 0.217
- R-Value Observed: 0.217
- Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.194 | α = 90 |
| b = 74.194 | β = 90 |
| c = 73.439 | γ = 120 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2005-04-05 Deposition Author(s): Ishijima, J., Yutani, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2005-04-05
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
