Download MendeleyA crystallographic fragment study with cAMP-dependent protein kinase A
Siefker, C., Heine, A., Klebe, G.To be published.
5N3M
cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule D-arginine
- PDB DOI: https://doi.org/10.2210/pdb5N3M/pdb
- Classification: TRANSFERASE
- Organism(s): Cricetulus griseus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-02-08 Released: 2018-02-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.23 ?
- R-Value Free: 0.164
- R-Value Work: 0.139
- R-Value Observed: 0.140
Starting Model: experimental
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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 |
| cAMP-dependent protein kinase catalytic subunit alpha | 353 | Cricetulus griseus | Mutation(s): 0 Gene Names: PRKACA EC: 2.7.11.11 |  | |
UniProt | |||||
Find proteins for P25321 (Cricetulus griseus) Explore P25321 Go to UniProtKB: P25321 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P25321 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DAR Query on DAR | G [auth A] | D-ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-SCSAIBSYSA-O |  | ||
| MPD Query on MPD | B [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| DMS Query on DMS | C [auth A], D [auth A], E [auth A], F [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SEP Query on SEP | A | L-PEPTIDE LINKING | C3 H8 N O6 P |  | SER |
| TPO Query on TPO | A | L-PEPTIDE LINKING | C4 H10 N O6 P |  | THR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.23 ?
- R-Value Free: 0.164
- R-Value Work: 0.139
- R-Value Observed: 0.140
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 51.979 | ¦Á = 90 |
| b = 71.002 | ¦Â = 90 |
| c = 97.552 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2018-02-28 Deposition Author(s): Siefker, C., Heine, A., Klebe, G.
Revision History (Full details and data files)
- Version 1.0: 2018-02-28
Type: Initial release - Version 1.1: 2019-08-14
Changes: Data collection - Version 1.2: 2019-09-18
Changes: Data collection - Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description - Version 1.4: 2024-10-16
Changes: Structure summary
