7JIJ
ATP-bound AMP-activated protein kinase
- PDB DOI: https://doi.org/10.2210/pdb7JIJ/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Escherichia coli, Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2020-07-23 Released: 2021-07-28 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 5.50 Å
- R-Value Free: 0.323 
- R-Value Work: 0.249 
- R-Value Observed: 0.253 
wwPDB Validation   3D Report Full Report
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Maltose/maltodextrin ABC transporter substrate-binding protein MalE | A [auth M] | 373 | Escherichia coli | Mutation(s): 0  Gene Names: malE, GRW33_05015 | |
UniProt | |||||
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0AEX9 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
5'-AMP-activated protein kinase catalytic subunit alpha-1 | B [auth A] | 484 | Homo sapiens | Mutation(s): 0  Gene Names: PRKAA1, AMPK1 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data) | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q13131 (Homo sapiens) Explore Q13131  Go to UniProtKB:  Q13131 | |||||
PHAROS:  Q13131 GTEx:  ENSG00000132356  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q13131 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
5'-AMP-activated protein kinase subunit beta-2 | C [auth B] | 198 | Homo sapiens | Mutation(s): 0  Gene Names: PRKAB2 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O43741 (Homo sapiens) Explore O43741  Go to UniProtKB:  O43741 | |||||
PHAROS:  O43741 GTEx:  ENSG00000131791  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O43741 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
5'-AMP-activated protein kinase subunit gamma-1 | D [auth G] | 306 | Homo sapiens | Mutation(s): 0  Gene Names: PRKAG1 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P54619 (Homo sapiens) Explore P54619  Go to UniProtKB:  P54619 | |||||
PHAROS:  P54619 GTEx:  ENSG00000181929  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P54619 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ATP Query on ATP | F [auth G] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N | |||
ADP Query on ADP | H [auth G] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N | |||
AMP Query on AMP | G | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
TPO Query on TPO | B [auth A] | L-PEPTIDE LINKING | C4 H10 N O6 P | THR |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900001 Query on PRD_900001 | E [auth C] | alpha-maltose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 5.50 Å
- R-Value Free: 0.323 
- R-Value Work: 0.249 
- R-Value Observed: 0.253 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 126.688 | α = 90 |
b = 126.688 | β = 90 |
c = 332.384 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-07-28  Deposition Author(s): Yan, Y., Zhou, X.E., Powell, K., Xu, T., Brunzelle, J.S., Xu, H.X., Melcher, K.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01 GM129436 |
Revision History (Full details and data files)
- Version 1.0: 2021-07-28
Type: Initial release - Version 1.1: 2021-09-08
Changes: Database references - Version 1.2: 2023-10-18
Changes: Data collection, Refinement description