1J1S

Pokeweed Antiviral Protein from Seeds (PAP-S1) Complexed with Formycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral Protein S261Phytolacca americanaMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P23339 (Phytolacca americana)
Explore P23339 
Go to UniProtKB:  P23339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23339
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMP
Query on FMP

Download Ideal Coordinates CCD File 
C [auth A]FORMYCIN-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
PBAHXXBYQACZMA-KSYZLYKTSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.164 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.1α = 90
b = 85.3β = 90
c = 92.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2024-11-06
    Changes: Structure summary