3UU1

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS142)

PDB DOI: https://doi.org/10.2210/pdb3UU1/pdb

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

Deposited: 2011-11-27 Released: 2012-12-12
Deposition Author(s): Castell, A., Short, F.L., Lott, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.256
R-Value Work: 0.212
R-Value Observed: 0.214

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: 157.62 kDa
Atom Count: 11,068
Modelled Residue Count: 1,354
Deposited Residue Count: 1,508
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, C, D	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRP Query on PRP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D]	E [auth A], I [auth B], N [auth C], S [auth D]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C₅ H₁₃ O₁₄ P₃ PQGCEDQWHSBAJP-TXICZTDVSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D]
14B Query on 14B Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D]	H [auth A] L [auth B] M [auth B] Q [auth C] R [auth C] H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], T [auth D]	2-amino-3,5-dimethylbenzoic acid C₉ H₁₁ N O₂ GIMYRAQQQBFFFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D]	F [auth A] G [auth A] J [auth B] K [auth B] O [auth C] F [auth A], G [auth A], J [auth B], K [auth B], O [auth C], P [auth C], U [auth D], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
14B	PDBBind: 3UU1	Ki: 6300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.256
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.226	α = 90
b = 110.962	β = 89.97
c = 80.382	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Castell, A.

Short, F.L.

Lott, J.S.

Revision History (Full details and data files)

Version 1.0: 2012-12-12
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: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

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3UU1

Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS142)

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)