5ZRN | pdb_00005zrn

Inhibitor bound crystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb5ZRN/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis CDC1551
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-24 Released: 2019-04-24
Deposition Author(s): Goyal, A., Sankaranarayanan, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.263 (Depositor), 0.250 (DCC)
R-Value Work:
0.198 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Inhibitor bound crystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis

Goyal, A., Sankaranarayanan, R.

To be published.

Macromolecule Content

Total Structure Weight: 87.29 kDa
Atom Count: 6,686
Modeled Residue Count: 796
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-chain-fatty-acid--CoA ligase FadD13	A, B	398	Mycobacterium tuberculosis CDC1551	Mutation(s): 0 Gene Names: fadD13, MT3174 EC: 6.2.1.3
UniProt
Find proteins for P9WQ37 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ37 Go to UniProtKB: P9WQ37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WQ37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JSA Query on JSA Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	5'-O-{[(1R)-1-hydroxydodecyl]sulfamoyl}adenosine C₂₂ H₃₈ N₆ O₇ S MDBNEGOGGFLHNH-FBLYDNEXSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.263 (Depositor), 0.250 (DCC)
R-Value Work: 0.198 (Depositor), 0.190 (DCC)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.647	α = 90
b = 129.647	β = 90
c = 185.965	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Sankaranarayanan, R.

Funding Organization	Location	Grant Number
	India	--

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.