Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 132.79 kDa 
• Atom Count: 9,308 
• Modelled Residue Count: 1,119 
• Deposited Residue Count: 1,185 
• Unique protein chains: 1

 7OOK

Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ

• PDB DOI: 10.2210/pdb7OOK/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Enterobacteria phage PRD1
• Mutation(s): No 


• Deposited: 2021-05-27 Released: 2022-06-08 
• Deposition Author(s): Duyvesteyn, H.M.E., Peccati, F., Martinez-Castillo, A., Jimenez-Oses, G., Oksanen, H.M., Stuart, D.I., Abrescia, N.G.A.
• Funding Organization(s): Ministry of Economy and Competitiveness (MINECO), Medical Research Council (MRC, United Kingdom), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Bacteriophage PRD1 as a nanoscaffold for drug loading

Duyvesteyn, H.M.E., Santos-Perez, I., Peccati, F., Martinez-Castillo, A., Walter, T.S., Reguera, D., Goni, F.M., Jimenez-Oses, G., Oksanen, H.M., Stuart, D.I., Abrescia, N.G.A.

(2021) Nanoscale 13: 19875-19883

• DOI: 10.1039/D1NR04153C

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein P3	C [auth A], B, A [auth C]	395	Enterobacteria phage PRD1	Mutation(s): 0  Gene Names: III
UniProt
Find proteins for P22535 (Enterobacteria phage PRD1) Explore P22535  Go to UniProtKB:  P22535

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z80 (Subject of Investigation/LOI)	H [auth B], Q [auth A], S [auth A]	3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine C17 H19 Cl N2 S ZPEIMTDSQAKGNT-UHFFFAOYSA-N
MPD	E [auth C], F [auth C], G [auth B], K [auth B], L [auth B], M [auth B], N [auth B], R [auth A], V [auth A], W [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	O [auth B], P [auth B], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth C], I [auth B], J [auth B], U [auth A], X [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.75	α = 90
b = 122.75	β = 90
c = 126.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Duyvesteyn, H.M.E., Peccati, F., Martinez-Castillo, A., Jimenez-Oses, G., Oksanen, H.M., Stuart, D.I., Abrescia, N.G.A.

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Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness (MINECO)	Spain	RTI2018-095700-B-I00
Ministry of Economy and Competitiveness (MINECO)	Spain	RTI2018-099592-B-C22
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1
Wellcome Trust	United Kingdom	ALR00750
Ministry of Economy and Competitiveness (MINECO)	Spain	SEV-2016-0644

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2022-07-13
  Changes: Database references
• Version 1.2: 2022-12-07
  Changes: Database references, Structure summary