Download MendeleyCrystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra)
Lin, C.C., Wu, B.S., Wu, W.G.To be published.
5GZ4
Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra)
- PDB DOI: https://doi.org/10.2210/pdb5GZ4/pdb
- Classification: HYDROLASE
- Organism(s): Naja atra
- Mutation(s): No
- Deposited: 2016-09-26 Released: 2017-09-27
- Funding Organization(s): MOST
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.288
- R-Value Work: 0.235
- R-Value Observed: 0.237
Starting Model: experimental
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This is version 2.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Snake venom phosphodiesterase (PDE) | 830 | Naja atra | Mutation(s): 0 EC: 3.6.1 |  | |
UniProt | |||||
Find proteins for A0A2D0TC04 (Naja atra) Explore A0A2D0TC04 Go to UniProtKB: A0A2D0TC04 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2D0TC04 | ||||
Glycosylation | |||||
| Glycosylation Sites: 6 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | B | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO | |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | H [auth A], I [auth A], J [auth A], K [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| ZN Query on ZN | D [auth A], E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.288
- R-Value Work: 0.235
- R-Value Observed: 0.237
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 171.679 | α = 90 |
| b = 65.876 | β = 90 |
| c = 89.615 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| MOST | Taiwan | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-09-27
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
