1J1R | pdb_00001j1r

Structure of Pokeweed Antiviral Protein from Seeds (PAP-S1) Complexed with Adenine

• PDB DOI: https://doi.org/10.2210/pdb1J1R/pdb

• Classification: HYDROLASE
• Organism(s): Phytolacca americana
• Mutation(s): No 


• Deposited: 2002-12-14 Released: 2004-02-03 
• Deposition Author(s): Watanabe, K., Sato, E., Honjo, E., Motoshima, H., Kurokawa, H., Mikami, B., Monzingo, A.F., Robertus, J.D., Fujii, H., Hidaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.172 (DCC) 

Literature

Crystal Structure of Pokweed Antiviral Protein from Seeds (PAP-S1) at 1.8 Angstrom Resolution

Watanabe, K., Sato, E., Honjo, E., Motoshima, H., Kurokawa, H., Mikami, B., Monzingo, A.F., Robertus, J.D., Fujii, H., Hidaka, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.59 kDa 
• Atom Count: 2,280 
• Modeled Residue Count: 261 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiviral Protein S	A	261	Phytolacca americana	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P23339 (Phytolacca americana) Explore P23339  Go to UniProtKB:  P23339
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ADE	C [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.172 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 85.3	β = 90
c = 92.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
X-PLOR	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-03 
Deposition Author(s): Watanabe, K., Sato, E., Honjo, E., Motoshima, H., Kurokawa, H., Mikami, B., Monzingo, A.F., Robertus, J.D., Fujii, H., Hidaka, A.

Revision History  

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2024-11-20
  Changes: Structure summary