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), 0.264 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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), 0.264 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (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

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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

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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.