2Q8W | pdb_00002q8w

Crystal structure of PAP-S1aci, a pokeweed antiviral protein from seeds of Phytolacca acinosa

• PDB DOI: https://doi.org/10.2210/pdb2Q8W/pdb

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


• Deposited: 2007-06-12 Released: 2008-06-17 
• Deposition Author(s): Hogg, T., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.177 (DCC) 

Starting Model: experimental

Literature

The complete covalent structure and 1.7 A crystal structure of PAP-S1aci reveals a RIP glycoprotein with multiple Asn-GlcNAc modifications

Hogg, T., Bezouska, K., Ulbrich, N., Kuta Smatanova, I., Hilgenfeld, R.

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: 29.54 kDa 
• Atom Count: 2,581 
• Modeled Residue Count: 261 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POKEWEED ANTIVIRAL PROTEIN	A	261	Phytolacca acinosa	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for D0VWY1 (Phytolacca acinosa) Explore D0VWY1  Go to UniProtKB:  D0VWY1
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.177 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.63	α = 90
b = 84.19	β = 90
c = 90.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Hogg, T., Hilgenfeld, R.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-06
  Changes: Structure summary