4GIU

Bianthranilate-like analogue bound in inner site of anthranilate phosphoribosyltransferase (AnPRT; trpD).

PDB DOI: https://doi.org/10.2210/pdb4GIU/pdb

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

Deposited: 2012-08-09 Released: 2013-08-14
Deposition Author(s): Evans, G.L., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.223
R-Value Work: 0.199
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 79.93 kDa
Atom Count: 5,679
Modelled Residue Count: 692
Deposited Residue Count: 756
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	378	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 5 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 L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B]	C [auth A], L [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 L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
636 Query on 636 Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A]	F [auth A], O [auth B]	2-[(2-carboxy-5-methylphenyl)amino]-3-methylbenzoic acid C₁₆ H₁₅ N O₄ AQDGEUMMMQRBPR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	G [auth A] H [auth A] I [auth A] P [auth B] Q [auth B] G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	J [auth A], K [auth A], S [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A], E [auth A], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
636	Binding MOAD: 4GIU	Ki: 4700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.223
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.442	α = 90
b = 80.752	β = 90
c = 78.723	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-14

Deposition Author(s):

Evans, G.L.

Baker, E.N.

Lott, J.S.

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2013-08-14
Type: Initial release
Version 1.1: 2014-05-21
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4GIU

Bianthranilate-like analogue bound in inner site of anthranilate phosphoribosyltransferase (AnPRT; trpD).

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)