Download MendeleyCrystal structure of the human Phosphodiesterase 9A catalytic domain
Handa, N., Shirouzu, M., Terada, T., Omori, K., Kotera, J., Yokoyama, S.To be published.
2YY2
Crystal structure of the human Phosphodiesterase 9A catalytic domain complexed with IBMX
- PDB DOI: https://doi.org/10.2210/pdb2YY2/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2007-04-27 Released: 2007-10-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.240
- R-Value Work: 0.206
- R-Value Observed: 0.206
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 |
| High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | 333 | Homo sapiens | Mutation(s): 0 EC: 3.1.4.35 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O76083 (Homo sapiens) Explore O76083 Go to UniProtKB: O76083 | |||||
PHAROS: O76083 GTEx: ENSG00000160191 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O76083 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IBM Query on IBM | E [auth A], H [auth B] | 3-ISOBUTYL-1-METHYLXANTHINE C10 H14 N4 O2 APIXJSLKIYYUKG-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A], F [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], G [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.240
- R-Value Work: 0.206
- R-Value Observed: 0.206
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 104.27 | α = 90 |
| b = 104.27 | β = 90 |
| c = 269.61 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-10-30 Deposition Author(s): Handa, N., Shirouzu, M., Terada, T., Omori, K., Kotera, J., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2007-10-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
