6CQC

RNase P protein from Thermotoga maritima in complex with 1-(4-Fluorophenyl)-2-thiourea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel RNase P inhibitors via an activity-binding-structure pipeline

Madrigal-Carrillo, E.A.Diaz-Tufinio, C.A.Santamaria-Suarez, H.A.Arciniega-Castro, M.Torres-Larios, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein component
A, B, C, D
118Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: rnpATM_1463
EC: 3.1.26.5
UniProt
Find proteins for Q9X1H4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1H4 
Go to UniProtKB:  Q9X1H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1H4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8P4
Query on 8P4

Download Ideal Coordinates CCD File 
Q [auth D]1-(4-fluorophenyl)thiourea
C7 H7 F N2 S
BRWKXKNZRVALNZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.136α = 90
b = 64.264β = 101.63
c = 68.121γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoPDCPN2014- 47543

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description