8BIK

Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455

PDB DOI: https://doi.org/10.2210/pdb8BIK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-11-02 Released: 2024-05-15
Deposition Author(s): Schimpl, M., Mather, K.M., Boland, M.L., Rivers, E.L., Srivastava, A., Hemsley, P., Robinson, J., Wan, P.T., Hansen, J., Read, J.A., Trevaskis, J.L., Smith, D.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.215
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Direct beta 1/ beta 2 AMPK activation reduces liver steatosis but not fibrosis in a mouse model of non-alcoholic steatohepatitis

Mather, K.M., Boland, M.L., Rivers, E.L., Srivastava, A., Schimpl, M., Hemsley, P., Robinson, J., Wan, P., Hansen, J., Read, J.A., Trevaskis, J.L., Smith, D.M.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.05.30.596624

Macromolecule Content

Total Structure Weight: 266.75 kDa
Atom Count: 15,482
Modelled Residue Count: 1,846
Deposited Residue Count: 2,320
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-2	A, D	559	Homo sapiens	Mutation(s): 0 Gene Names: PRKAA2, AMPK, AMPK2 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P54646 (Homo sapiens) Explore P54646 Go to UniProtKB: P54646
PHAROS: P54646 GTEx: ENSG00000162409
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54646
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-1	B, E	270	Homo sapiens	Mutation(s): 0 Gene Names: PRKAB1, AMPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens) Explore Q9Y478 Go to UniProtKB: Q9Y478
PHAROS: Q9Y478 GTEx: ENSG00000111725
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y478
Sequence Annotations Expand
Reference Sequence

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 gamma-1	C, F	331	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QTN Query on QTN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth D]	H [auth A], L [auth D]	(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol C₂₆ H₂₇ Cl N₄ O₅ S LFEPFIOGKSTJHX-LUGTWXOSSA-N		Interactions Focus chain H [auth A] Focus chain L [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth D]
STU Query on STU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth D]	G [auth A], K [auth D]	STAUROSPORINE C₂₈ H₂₆ N₄ O₃ HKSZLNNOFSGOKW-FYTWVXJKSA-N		Interactions Focus chain G [auth A] Focus chain K [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth D]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain M [auth F] SDF format, chain N [auth F] SDF format, chain O [auth F] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F] mmCIF format, chain O [auth F]	I [auth C], J [auth C], M [auth F], N [auth F], O [auth F]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth F] Focus chain N [auth F] Focus chain O [auth F]