5CLT | pdb_00005clt

Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose

• PDB DOI: https://doi.org/10.2210/pdb5CLT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2015-08-12 
• Deposition Author(s): Krojer, T., Froese, D.S., Goubin, S., Strain-Damerell, C., Mahajan, P., Burgess-Brown, N., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose

Krojer, T., Froese, D.S., Goubin, S., Strain-Damerell, C., Mahajan, P., Burgess-Brown, N., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 233.05 kDa 
• Atom Count: 15,456 
• Modeled Residue Count: 1,920 
• Deposited Residue Count: 2,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-alpha-glucan-branching enzyme	A, B, C	668	Homo sapiens	Mutation(s): 0  Gene Names: GBE1 EC: 2.4.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q04446 (Homo sapiens) Explore Q04446  Go to UniProtKB:  Q04446
PHAROS:  Q04446 GTEx:  ENSG00000114480

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-alpha-D-glucopyranose	D, E, F	3	N/A	N/A
Glycosylation Resources
GlyTouCan: G66431MI GlyCosmos: G66431MI

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007	D, E, F	alpha-acarbose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.76	α = 90
b = 163.99	β = 90
c = 311.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Krojer, T., Froese, D.S., Goubin, S., Strain-Damerell, C., Mahajan, P., Burgess-Brown, N., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Yue, W., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary