2UV6

Crystal Structure of a CBS domain pair from the regulatory gamma1 subunit of human AMPK in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb2UV6/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-03-09 Released: 2007-05-08
Deposition Author(s): Day, P., Sharff, A., Parra, L., Cleasby, A., Williams, M., Horer, S., Nar, H., Redemann, N., Tickle, I., Yon, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.172
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of a Cbs-Domain Pair from the Regulatory Gamma1 Subunit of Human Ampk in Complex with AMP and Zmp.

Day, P., Sharff, A., Parra, L., Cleasby, A., Williams, M., Horer, S., Nar, H., Redemann, N., Tickle, I., Yon, J.

(2007) Acta Crystallogr D Biol Crystallogr 63: 587

PubMed: 17452784 Search on PubMed
DOI: https://doi.org/10.1107/S0907444907009110
Primary Citation of Related Structures:
2UV4, 2UV5, 2UV6, 2UV7

PubMed Abstract:
AMP-activated kinase (AMPK) is central to sensing energy status in eukaryotic cells via binding of AMP and ATP to CBS (cystathionine beta-synthase) domains in the regulatory gamma subunit. The structure of a CBS-domain pair from human AMPK gamma1 in complex with the physiological activator AMP and the pharmacological activator ZMP (AICAR) is presented.

Organizational Affiliation

Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, England. [email protected]

Macromolecule Content

Total Structure Weight: 17.6 kDa
Atom Count: 1,359
Modelled Residue Count: 144
Deposited Residue Count: 152
Unique protein chains: 1

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 SUBUNIT GAMMA-1	A	152	Homo sapiens	Mutation(s): 1
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
AMP	BindingDB: 2UV6	Kd: 3700 (nM) from 1 assay(s)
AMP	BindingDB: 2UV6	EC50: min: 1400, max: 1519 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.172
R-Value Observed: 0.176
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.092	α = 90
b = 43.775	β = 119.04
c = 55.786	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-08
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Other