6GNG

Granule Bound Starch Synthase I from Cyanophora paradoxa bound to acarbose and ADP

• PDB DOI: https://doi.org/10.2210/pdb6GNG/pdb

• Classification: TRANSFERASE
• Organism(s): Cyanophora paradoxa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-30 Released: 2018-07-25 
• Deposition Author(s): Cuesta-Seijo, J.A., Nielsen, M.M., Palcic, M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.303 
• R-Value Work: 0.272 
• R-Value Observed: 0.273 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 134.91 kDa 
• Atom Count: 8,253 
• Modelled Residue Count: 1,051 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Granule-bound starch synthase	A, B	612	Cyanophora paradoxa	Mutation(s): 0
UniProt
Find proteins for A8V967 (Cyanophora paradoxa) Explore A8V967  Go to UniProtKB:  A8V967

Oligosaccharides

Help

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
Glycosylation Resources
GlyTouCan:  G08743RW GlyCosmos:  G08743RW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900022	C, D	beta-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.303 
• R-Value Work: 0.272 
• R-Value Observed: 0.273 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.3	α = 90
b = 106.1	β = 90
c = 175.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Cuesta-Seijo, J.A., Nielsen, M.M., Palcic, M.M.

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Funding Organization	Location	Grant Number
	Denmark	--

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• 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: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary