5FU0 | pdb_00005fu0

Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

PDB DOI: https://doi.org/10.2210/pdb5FU0/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-19 Released: 2017-02-22
Deposition Author(s): Alphey, M.S., Tran, F., Westwood, N.J., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.285 (Depositor), 0.290 (DCC)
R-Value Work:
0.253 (Depositor), 0.260 (DCC)
R-Value Observed:
0.255 (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

Allosteric Competitive Inhibitors of the Glucose-1-Phosphate Thymidylyltransferase (Rmla) from Pseudomonas Aeruginosa.

Tran, F., Alphey, M.S., Westwood, N.J., Naismith, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 137.18 kDa
Atom Count: 10,385
Modeled Residue Count: 1,177
Deposited Residue Count: 1,212
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE	A, B, C, D	303	Pseudomonas aeruginosa	Mutation(s): 0 EC: 2.7.7.24
UniProt
Find proteins for Q9HU22 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HU22 Go to UniProtKB: Q9HU22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HU22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FKH Query on FKH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	N-(6-AMINO-1-(3-METHYLBENZYL)-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-N-METHYLBENZENESULFONAMIDE C₁₉ H₂₀ N₄ O₄ S RDABNCDTRJGKTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.285 (Depositor), 0.290 (DCC)
R-Value Work: 0.253 (Depositor), 0.260 (DCC)
R-Value Observed: 0.255 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.15	α = 90
b = 154.35	β = 92.41
c = 134.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2017-07-05
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Help and Resources

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Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor

Allosteric Competitive Inhibitors of the Glucose-1-Phosphate Thymidylyltransferase (Rmla) from Pseudomonas Aeruginosa.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations