7OOK | pdb_00007ook

Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ

PDB DOI: https://doi.org/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.176 (Depositor), 0.174 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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: https://doi.org/10.1039/D1NR04153C

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein P3	A [auth C], B, C [auth A]	395	Enterobacteria phage PRD1	Mutation(s): 0
UniProt
Find proteins for P22535 (Enterobacteria phage PRD1) Explore P22535 Go to UniProtKB: P22535
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22535
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Z80 (Subject of Investigation/LOI) Query on Z80 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain Q [auth A] SDF format, chain S [auth A] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A]	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		Interactions Focus chain H [auth B] Focus chain Q [auth A] Focus chain S [auth A] Interactions & Density Focus chain H [auth B] Focus chain Q [auth A] Focus chain S [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	E [auth C] F [auth C] G [auth B] K [auth B] L [auth B] 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		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth A] Focus chain V [auth A] Focus chain W [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth A]	O [auth B], P [auth B], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth A] Interactions & Density Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain X [auth A] SDF format, chain U [auth A] MOL2 format, chain D [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain X [auth A] MOL2 format, chain U [auth A] mmCIF format, chain D [auth C] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain X [auth A] mmCIF format, chain U [auth A]	D [auth C], I [auth B], J [auth B], U [auth A], X [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain I [auth B] Focus chain J [auth B] Focus chain U [auth A] Focus chain X [auth A] Interactions & Density Focus chain D [auth C] Focus chain I [auth B] Focus chain J [auth B] Focus chain U [auth A] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.176 (Depositor), 0.174 (DCC)
R-Value Observed: 0.178 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-08

Deposition Author(s):

Duyvesteyn, H.M.E.

Peccati, F.

Martinez-Castillo, A.

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