6CQC | pdb_00006cqc

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

PDB DOI: https://doi.org/10.2210/pdb6CQC/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-03-14 Released: 2019-03-20
Deposition Author(s): Torres-Larios, A., Madrigal-Carrillo, E.A.
Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

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.

Macromolecule Content

Total Structure Weight: 59.06 kDa
Atom Count: 4,293
Modeled Residue Count: 430
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease P protein component	A, B, C, D	118	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: rnpA, TM_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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X1H4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8P4 Query on 8P4 Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	1-(4-fluorophenyl)thiourea C₇ H₇ F N₂ S BRWKXKNZRVALNZ-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.136	α = 90
b = 64.264	β = 101.63
c = 68.121	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Torres-Larios, A.

Madrigal-Carrillo, E.A.

Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	PDCPN2014- 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