1VIW | pdb_00001viw

TENEBRIO MOLITOR ALPHA-AMYLASE-INHIBITOR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1VIW/pdb

• Classification: COMPLEX (GLYCOSIDASE/INHIBITOR)
• Organism(s): Tenebrio molitor, Phaseolus vulgaris
• Mutation(s): No 


• Deposited: 1998-07-21 Released: 1999-07-22 
• Deposition Author(s): Nahoum, V., Egloff, M.P., Payan, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.291 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: in silico

Literature

A plant-seed inhibitor of two classes of alpha-amylases: X-ray analysis of Tenebrio molitor larvae alpha-amylase in complex with the bean Phaseolus vulgaris inhibitor.

Nahoum, V., Farisei, F., Le-Berre-Anton, V., Egloff, M.P., Rouge, P., Poerio, E., Payan, F.

(1999) Acta Crystallogr D Biol Crystallogr 55: 360-362

• PubMed: 10089450 
• DOI: https://doi.org/10.1107/S0907444998010701
• Primary Citation of Related Structures:  
  1VIW


• PubMed Abstract: 
  

  The alpha-amylase from Tenebrio molitor larvae (TMA) has been crystallized in complex with the alpha-amylase inhibitor (alpha-AI) from the bean Phaseolus vulgaris. A molecular-replacement solution of the structure was obtained using the refined pig pancreatic alpha-amylase (PPA) and alpha-AI atomic coordinates as starting models. The structural analysis showed that although TMA has the typical structure common to alpha-amylases, large deviations from the mammalian alpha-amylase models occur in the loops. Despite these differences in the interacting loops, the bean inhibitor is still able to inhibit both the insect and mammalian alpha-amylase.

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Organizational Affiliation: 

AFMB-IBSM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.87 kDa 
• Atom Count: 5,218 
• Modelled Residue Count: 669 
• Deposited Residue Count: 676 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-AMYLASE	A	471	Tenebrio molitor	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for P56634 (Tenebrio molitor) Explore P56634  Go to UniProtKB:  P56634

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-AMYLASE-INHIBITOR	B	205	Phaseolus vulgaris	Mutation(s): 0
UniProt
Find proteins for P02873 (Phaseolus vulgaris) Explore P02873  Go to UniProtKB:  P02873
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.291 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.475	α = 90
b = 75.911	β = 101.29
c = 61.989	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-22 
Deposition Author(s): Nahoum, V., Egloff, M.P., Payan, F.

Revision History  

• Version 1.0: 1999-07-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2016-03-30
  Changes: Other
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.2: 2024-10-30
  Changes: Structure summary