6QMI | pdb_00006qmi

Phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 3-(1H-indol-1-yl)propanoic acid at 1.7A resolution.

PDB DOI: https://doi.org/10.2210/pdb6QMI/pdb
Entry: 6QMI supersedes: 6G7S

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

Deposited: 2019-02-07 Released: 2020-02-26
Deposition Author(s): Blaszczyk, M., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.282 (Depositor), 0.242 (DCC)
R-Value Work:
0.245 (Depositor), 0.247 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Fragment linking applied to the discovery of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase inhibitors

Blaszczyk, M., El Bakali, J., Boland, J.A., Spry, C., Dias, M., Blundell, T.L., Abel, C.

To be published.

Macromolecule Content

Total Structure Weight: 17.99 kDa
Atom Count: 1,215
Modeled Residue Count: 146
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	163	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: coaD, kdtB, Rv2965c, MTCY349.22, u0002e EC: 2.7.7.3
UniProt
Find proteins for P9WPA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPA5 Go to UniProtKB: P9WPA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9FH Query on 9FH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-methyl-1-phenyl-pyrazole-4-carboxylic acid C₁₁ H₁₀ N₂ O₂ USSMIQWDLWJQDQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.282 (Depositor), 0.242 (DCC)
R-Value Work: 0.245 (Depositor), 0.247 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.994	α = 90
b = 97.994	β = 90
c = 113.956	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

This entry supersedes: 6G7S

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.