3R88

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS145)

PDB DOI: https://doi.org/10.2210/pdb3R88/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-23 Released: 2012-09-26
Deposition Author(s): Castell, A., Short, F.L., Lott, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.214
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 78.6 kDa
Atom Count: 5,733
Modelled Residue Count: 688
Deposited Residue Count: 754
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A, B	377	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT2248, MTCY190.03c, Rv2192c, trpD EC: 2.4.2.18
UniProt
Find proteins for P9WFX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX5 Go to UniProtKB: P9WFX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WFX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRP Query on PRP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C₅ H₁₃ O₁₄ P₃ PQGCEDQWHSBAJP-TXICZTDVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
14F Query on 14F Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	2-amino-4,5-dimethoxybenzoic acid C₉ H₁₁ N O₄ HJVAVGOPTDJYOJ-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
14F	PDBBind: 3R88	Ki: 1.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.214
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.312	α = 90
b = 78.849	β = 110.27
c = 100.494	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Castell, A.

Short, F.L.

Lott, J.S.

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2013-02-20
Changes: Database references
Version 1.2: 2013-04-10
Changes: Database references
Version 1.3: 2013-11-27
Changes: Database references
Version 1.4: 2017-11-08
Changes: Refinement description
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.6: 2024-02-21
Changes: Data collection, Database references, Structure summary

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Help and Resources

3R88

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS145)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)