2B9L

Crystal structure of prophenoloxidase activating factor-II from the beetle Holotrichia diomphalia

• PDB DOI: https://doi.org/10.2210/pdb2B9L/pdb

• Classification: IMMUNE SYSTEM/PROTEIN BINDING
• Organism(s): Holotrichia diomphalia
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-10-12 Released: 2006-01-03 
• Deposition Author(s): Piao, S., Song, Y.-L., Park, S.Y., Lee, B.L., Oh, B.-H., Ha, N.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.38 kDa 
• Atom Count: 3,215 
• Modelled Residue Count: 372 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
prophenoloxidase activating factor	A	394	Holotrichia diomphalia	Mutation(s): 0
UniProt
Find proteins for Q9GRW0 (Holotrichia diomphalia) Explore Q9GRW0  Go to UniProtKB:  Q9GRW0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G63564LA GlyCosmos:  G63564LA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.78	α = 90
b = 76.587	β = 113.45
c = 69.833	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-03 
Deposition Author(s): Piao, S., Song, Y.-L., Park, S.Y., Lee, B.L., Oh, B.-H., Ha, N.-C.

Revision History  

• Version 1.0: 2006-01-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary