5ISO | pdb_00005iso

STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991)

PDB DOI: https://doi.org/10.2210/pdb5ISO/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-15 Released: 2017-03-29
Deposition Author(s): Xiao, B., Hubbard, J.A., Gamblin, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.230 (Depositor), 0.235 (DCC)
R-Value Work:
0.178 (Depositor), 0.191 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991)

Xiao, B., Hubbard, J.A., Gamblin, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 268.85 kDa
Atom Count: 14,898
Modeled Residue Count: 1,835
Deposited Residue Count: 2,338
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-2	A, D [auth C]	552	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54646
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-1	B, E [auth D]	286	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y478
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit gamma-1	C [auth E], 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54619
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STU Query on STU Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C]	G [auth A], L [auth C]	STAUROSPORINE C₂₈ H₂₆ N₄ O₃ HKSZLNNOFSGOKW-FYTWVXJKSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]
992 Query on 992 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain H [auth A]	H [auth A], M [auth C]	5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid C₂₄ H₁₈ Cl N₃ O₃ FHWSAZXFPUMKFL-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth C]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain J [auth E] SDF format, chain K [auth E] SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain N [auth F] MOL2 format, chain I [auth E] MOL2 format, chain J [auth E] MOL2 format, chain K [auth E] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain N [auth F] mmCIF format, chain I [auth E] mmCIF format, chain J [auth E] mmCIF format, chain K [auth E] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain N [auth F]	I [auth E] J [auth E] K [auth E] N [auth F] O [auth F] I [auth E], J [auth E], K [auth E], N [auth F], O [auth F], P [auth F]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth E] Focus chain J [auth E] Focus chain K [auth E] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain I [auth E] Focus chain J [auth E] Focus chain K [auth E] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	B, E [auth D]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.230 (Depositor), 0.235 (DCC)
R-Value Work: 0.178 (Depositor), 0.191 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.42	α = 90
b = 129.39	β = 92.73
c = 139.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Xiao, B.

Hubbard, J.A.

Gamblin, S.J.

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2019-06-12
Changes: Data collection, Database references, Structure summary
Version 1.2: 2019-10-16
Changes: Data collection
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary