6P7U | pdb_00006p7u

CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD6) IN COMPLEX WITH INHIBITOR QUIZALOFOP-P FROM MYCOBACTERIUM TUBERCULOSIS

PDB DOI: https://doi.org/10.2210/pdb6P7U/pdb

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

Deposited: 2019-06-06 Released: 2020-06-10
Deposition Author(s): Reddy, M.C.M., Sacchettini, J.C., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.206 (Depositor), 0.214 (DCC)
R-Value Work:
0.171 (Depositor), 0.179 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4G2R

Literature

Inhibition of Mycobacterium tuberculosis acetyl-CoA carboxyltransferase(AccD6)d omain of acetyl-coenzyme A carboxylase by quizalofop-p

Reddy, M.C.M., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 202.17 kDa
Atom Count: 13,244
Modeled Residue Count: 1,688
Deposited Residue Count: 1,892
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable propionyl-CoA carboxylase beta chain 6	A, B, C, D	473	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: accD6, Rv2247, MTCY427.28 EC: 6.4.1.3 (PDB Primary Data), 2.1.3.15 (UniProt), 2.1.3 (UniProt)
UniProt
Find proteins for P9WQH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQH5 Go to UniProtKB: P9WQH5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WQH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FTJ (Subject of Investigation/LOI) Query on FTJ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	(2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic acid C₁₇ H₁₃ Cl N₂ O₄ ABOOPXYCKNFDNJ-SNVBAGLBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.206 (Depositor), 0.214 (DCC)
R-Value Work: 0.171 (Depositor), 0.179 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.604	α = 90
b = 153.343	β = 90
c = 102.863	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Sacchettini, J.C.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-06-10
Type: Initial release
Version 1.1: 2023-10-11
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.