1LPD | pdb_00001lpd

HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTEIN-POTENT ANTI-HIV AGENT (COMPLEX WITH ADENINE)

• PDB DOI: https://doi.org/10.2210/pdb1LPD/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Dianthus caryophyllus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-07 Released: 2004-05-11 
• Deposition Author(s): Kurinov, I.V., Rajamohan, F., Uckun, F.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

High resolution X-ray structure and potent anti-HIV activity of recombinant dianthin antiviral protein.

Kurinov, I.V., Rajamohan, F., Uckun, F.M.

(2004) Arzneimittelforschung 54: 692-702

• PubMed: 15553110 
• DOI: https://doi.org/10.1055/s-0031-1297024
• Primary Citation Related Structures: 
  1LP8, 1LPC, 1LPD


• PubMed Abstract: 
  

  Dianthin antiviral protein (DAP) is a naturally occurring antiviral protein from the leaves of carnation (Dianthus caryophyllus) capable of depurinating HIV-1 RNA and inhibiting HIV-1 replication in human peripheral blood mononuclear cells. Escherichia coli-derived recombinant DAP (rDAP, amino acids 1-254) was purified to homogeneity for structural and functional studies. In the following paper the X-ray crystal structure of rDAP as well as its complexes with cyclic AMP and adenyl-guanosine (ApG) as substrate analogs at 1.7 A resolution are reported. Molecular modeling studies of the interactions of DAP and the structurally similar pokeweed antiviral protein (PAP) with a single-stranded RNA heptamer predicted a more potent anti-HIV activity for rDAP due to its unique surface topology and more favorable charge distribution in its 20 A-long RNA binding active center cleft. In accordance with the predictions of the modeling studies, rDAP was more potent than rPAP in depurinating HIV-1 RNA. To the knowledge of the authors, this is the first structural and functional characterization of recombinant DAP.

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Organizational Affiliation: 
• Biotherapy and Drug Discovery Program, Parker Hughes Institute, St Paul, Minnesota 55113, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.74 kDa 
• Atom Count: 2,212 
• Modeled Residue Count: 254 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dianthin 30	A	254	Dianthus caryophyllus	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P24476 (Dianthus caryophyllus) Explore P24476  Go to UniProtKB:  P24476

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	B [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.093	α = 90
b = 78.464	β = 105.26
c = 42.721	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-11 
Deposition Author(s): Kurinov, I.V., Rajamohan, F., Uckun, F.M.

Revision History  

• Version 1.0: 2004-05-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description