7OOK

Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein P3C [auth A],
B,
A [auth C]
395Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: III
UniProt
Find proteins for P22535 (Enterobacteria phage PRD1)
Explore P22535 
Go to UniProtKB:  P22535
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22535
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z80 (Subject of Investigation/LOI)
Query on Z80

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
O [auth B],
P [auth B],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth C],
I [auth B],
J [auth B],
U [auth A],
X [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 = 116.75α = 90
b = 122.75β = 90
c = 126.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainRTI2018-095700-B-I00
Ministry of Economy and Competitiveness (MINECO)SpainRTI2018-099592-B-C22
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited KingdomALR00750
Ministry of Economy and Competitiveness (MINECO)SpainSEV-2016-0644

Revision History  (Full details and data files)

  • 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