4BQI | pdb_00004bqi

ARABIDOPSIS THALIANA cytosolic alpha-1,4-glucan phosphorylase (PHS2) in complex with maltotriose

PDB DOI: https://doi.org/10.2210/pdb4BQI/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: 1.90 Å
R-Value Free:
0.241 (Depositor), 0.237 (DCC)
R-Value Work:
0.196 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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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: 199.83 kDa
Atom Count: 14,073
Modeled Residue Count: 1,648
Deposited Residue Count: 1,748
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SD76
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	3		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA

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 G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009 Query on PRD_900009	C, D	alpha-maltotriose	Oligosaccharide / Nutrient		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: 1.90 Å
R-Value Free: 0.241 (Depositor), 0.237 (DCC)
R-Value Work: 0.196 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.713	α = 90
b = 116.072	β = 107.38
c = 94.342	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

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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: 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