4BQF

Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with acarbose

PDB DOI: https://doi.org/10.2210/pdb4BQF/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-30 Released: 2014-02-19
Deposition Author(s): O'Neill, E.C., Rashid, A.M., Stevenson, C.E.M., Hetru, A.C., Gunning, A.P., Rejzek, M., Nepogodiev, S.A., Bornemann, S., Lawson, D.M., Field, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.240
R-Value Work: 0.184
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Sugar-Coated Sensor Chip and Nanoparticle Surfaces for the in Vitro Enzymatic Synthesis of Starch-Like Materials

O'Neill, E.C., Rashid, A.M., Stevenson, C.E.M., Hetru, A.C., Gunning, A.P., Rejzek, M., Nepogodiev, S.A., Bornemann, S., Lawson, D.M., Field, R.A.

(2014) Chem Sci 5: 341

DOI: https://doi.org/10.1039/C3SC51829A

Macromolecule Content

Total Structure Weight: 200.55 kDa
Atom Count: 13,573
Modelled Residue Count: 1,651
Deposited Residue Count: 1,748
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-GLUCAN PHOSPHORYLASE 2, CYTOSOLIC	A, B	874	Arabidopsis thaliana	Mutation(s): 0 EC: 2.4.1.1
UniProt
Find proteins for Q9SD76 (Arabidopsis thaliana) Explore Q9SD76 Go to UniProtKB: Q9SD76
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SD76
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	3	N/A	N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G08743RW GlyCosmos: G08743RW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B]	F [auth A], G [auth A], I [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900022 Query on PRD_900022	C, D	beta-acarbose	Oligosaccharide / Inhibitor		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.240
R-Value Work: 0.184
R-Value Observed: 0.187
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.249	α = 90
b = 117.075	β = 106.79
c = 94.967	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-19
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4BQF

Arabidopsis thaliana cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with acarbose

Sugar-Coated Sensor Chip and Nanoparticle Surfaces for the in Vitro Enzymatic Synthesis of Starch-Like Materials

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2