5BNE

Bianthranilate-like inhibitor with 6 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)

PDB DOI: https://doi.org/10.2210/pdb5BNE/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-26 Released: 2016-05-25
Deposition Author(s): Evans, G.L., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): Health Research Council (HRC), FRST (Foundation for Research, Science and Technology)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.235
R-Value Work: 0.207
R-Value Observed: 0.208

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Binding and mimicking of the phosphate-rich substrate, PRPP.

Evans, G.L., Baker, E.N., Lott, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 157.34 kDa
Atom Count: 9,740
Modelled Residue Count: 1,326
Deposited Residue Count: 1,516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A, B, C, D	379	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpD, Rv2192c, MTCY190.03c 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7P3 Query on 7P3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D]	E [auth A], G [auth B], K [auth D]	2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid C₁₉ H₂₂ N O₈ P HYMLLKWKTLKWNS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C]	F [auth A], H [auth B], I [auth B], J [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.235
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.3	α = 90
b = 78.4	β = 90.7
c = 117.2	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-05-25

Deposition Author(s):

Evans, G.L.

Baker, E.N.

Lott, J.S.

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	HRC12/1111
FRST (Foundation for Research, Science and Technology)	New Zealand	UOAX1005

Revision History (Full details and data files)

Version 1.0: 2016-05-25
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5BNE

Bianthranilate-like inhibitor with 6 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)

Binding and mimicking of the phosphate-rich substrate, PRPP.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)