5CSY

Disproportionating enzyme 1 from Arabidopsis - acarbose soak

PDB DOI: https://doi.org/10.2210/pdb5CSY/pdb

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

Deposited: 2015-07-23 Released: 2015-11-04
Deposition Author(s): O'Neill, E.C., Stevenson, C.E.M., Tantanarat, K., Latousakis, D., Donaldson, M.I., Rejzek, M., Limpaseni, T., Smith, A.M., Field, R.A., Lawson, D.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.210
R-Value Work: 0.187
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 129.63 kDa
Atom Count: 8,614
Modelled Residue Count: 1,023
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic	A, B	564	Arabidopsis thaliana	Mutation(s): 0 Gene Names: DPE1, At5g64860, MXK3.9 EC: 2.4.1.25
UniProt
Find proteins for Q9LV91 (Arabidopsis thaliana) Explore Q9LV91 Go to UniProtKB: Q9LV91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LV91
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	3		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G00395FS GlyCosmos: G00395FS GlyGen: G00395FS

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	4		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G69211UR GlyCosmos: G69211UR GlyGen: G69211UR

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-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)-alpha-D-glucopyranose	E	6	N/A	N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G35727IJ GlyCosmos: G35727IJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900065 Query on PRD_900065	C	beta-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.210
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.79	α = 64.59
b = 73.69	β = 69.99
c = 79.35	γ = 66.78

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J004561/1

Revision History (Full details and data files)

Version 1.0: 2015-11-04
Type: Initial release
Version 1.1: 2015-12-23
Changes: Database references
Version 1.2: 2017-08-30
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Help and Resources

5CSY

Disproportionating enzyme 1 from Arabidopsis - acarbose soak

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)