3H5K

Crystal structure of the ribosome inactivating protein PDL1

• PDB DOI: https://doi.org/10.2210/pdb3H5K/pdb

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


• Deposited: 2009-04-22 Released: 2009-10-13 
• Deposition Author(s): Ruggiero, A., Di Maro, A., Severino, V., Chambery, A., Berisio, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.242 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.07 kDa 
• Atom Count: 5,002 
• Modelled Residue Count: 522 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-inactivating protein PD-L1/PD-L2	A, B	261	Phytolacca dioica	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P84853 (Phytolacca dioica) Explore P84853  Go to UniProtKB:  P84853

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.242 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.011	α = 90
b = 34.735	β = 127.99
c = 120.63	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REMO	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REMO	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Ruggiero, A., Di Maro, A., Severino, V., Chambery, A., Berisio, R.

Revision History  

• Version 1.0: 2009-10-13
  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