4END

Crystal structure of anti-HIV actinohivin in complex with alpha-1,2-mannobiose (P 2 21 21 form)

• PDB DOI: https://doi.org/10.2210/pdb4END/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): actinomycete K97-0003
• Mutation(s): No 


• Deposited: 2012-04-13 Released: 2013-07-17 
• Deposition Author(s): Hoque, M.M., Suzuki, K., Tsunoda, M., Jiang, J., Zhang, F., Takahashi, A., Naomi, O., Zhang, X., Sekiguchi, T., Tanaka, H., Omura, S., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Matured structure of anti-HIV lectin actinohivin in complex with 1,2-mannobiose

Hoque, M.M., Suzuki, K., Tsunoda, M., Jiang, J., Zhang, F., Takahashi, A., Naomi, O., Zhang, X., Sekiguchi, T., Tanaka, H., Omura, S., Takenaka, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 13.64 kDa 
• Atom Count: 1,105 
• Modelled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinohivin	A	114	actinomycete K97-0003	Mutation(s): 0
UniProt
Find proteins for Q9KWN0 (Actinomycete sp. (strain K97-0003)) Explore Q9KWN0  Go to UniProtKB:  Q9KWN0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	B, C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CCN	E [auth A], F [auth A]	ACETONITRILE C2 H3 N WEVYAHXRMPXWCK-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	B, C, D	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.84	α = 90
b = 66.84	β = 90
c = 67.06	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Hoque, M.M., Suzuki, K., Tsunoda, M., Jiang, J., Zhang, F., Takahashi, A., Naomi, O., Zhang, X., Sekiguchi, T., Tanaka, H., Omura, S., Takenaka, A.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• 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: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary