Download MendeleyPKA based studies of ligand interactions with a methionine gatekeeper.
Narayanan, D., Gani, O.A., Alam, K.A., Engh, R.A.To be published.
5BX7
PKA in complex with a benzothiophene fragment compound.
- PDB DOI: https://doi.org/10.2210/pdb5BX7/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-06-08 Released: 2016-09-14
- Funding Organization(s): FRINAT
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.89 Å
- R-Value Free: 0.226
- R-Value Work: 0.175
- R-Value Observed: 0.178
Starting Model: experimental
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This is version 1.1 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 | 351 | Homo sapiens | Mutation(s): 0 Gene Names: PRKACA, PKACA EC: 2.7.11.11 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P17612 (Homo sapiens) Explore P17612 Go to UniProtKB: P17612 | |||||
PHAROS: P17612 GTEx: ENSG00000072062 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P17612 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| cAMP-dependent protein kinase inhibitor alpha | 20 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61925 (Homo sapiens) Explore P61925 Go to UniProtKB: P61925 | |||||
PHAROS: P61925 GTEx: ENSG00000171033 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61925 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 4W1 Query on 4W1 | C [auth A] | 1-benzothiophen-3-ylmethanol C9 H8 O S UYGMKSKKGSUAHB-UHFFFAOYSA-N |  | ||
| MPD Query on MPD | D [auth A], F [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| EDO Query on EDO | E [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.89 Å
- R-Value Free: 0.226
- R-Value Work: 0.175
- R-Value Observed: 0.178
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.653 | α = 90 |
| b = 75.417 | β = 90 |
| c = 80.54 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Coot | model building |
| MOLREP | phasing |
| Aimless | data scaling |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-09-14 Deposition Author(s): Narayanan, D., Alam, K.A., Engh, R.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| FRINAT | Norway | 191303 |
Revision History (Full details and data files)
- Version 1.0: 2016-09-14
Type: Initial release - Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
