4YEF

beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin

PDB DOI: https://doi.org/10.2210/pdb4YEF/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-24 Released: 2015-06-24
Deposition Author(s): Mobbs, J., Gorman, M.A., Parker, M.W., Gooley, P.R., Griffin, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.213
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 78.2 kDa
Atom Count: 6,310
Modelled Residue Count: 559
Deposited Residue Count: 623
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 beta-1	A, B, C, D, E A, B, C, D, E, F, G	89	Rattus norvegicus	Mutation(s): 0 Gene Names: Prkab1
UniProt
Find proteins for P80386 (Rattus norvegicus) Explore P80386 Go to UniProtKB: P80386
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80386
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	H, I, J, K, L H, I, J, K, L, M, N	7		N/A	Interactions Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G01435GL GlyCosmos: G01435GL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F]	P [auth B] Q [auth B] S [auth D] T [auth E] U [auth E] P [auth B], Q [auth B], S [auth D], T [auth E], U [auth E], V [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain O [auth A] MOL2 format, chain R [auth C] MOL2 format, chain O [auth A]	O [auth A], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain R [auth C] Interactions & Density Focus chain O [auth A] Focus chain R [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012 Query on PRD_900012	H, I, J, K, L H, I, J, K, L, M, N	beta-cyclodextrin	Oligosaccharide / Drug delivery		Interactions Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.213
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.718	α = 111.72
b = 68.394	β = 95.56
c = 92.211	γ = 90.06

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
Aimless	data scaling
XDS	data reduction
Blu-Ice	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2020-05-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 3.0: 2022-04-13
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 3.1: 2023-09-27
Changes: Data collection, Refinement description

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Help and Resources

4YEF

beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)