5ICR | pdb_00005icr

2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from Mycobacterium smegmatis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine.

PDB DOI: https://doi.org/10.2210/pdb5ICR/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-23 Released: 2016-04-06
Deposition Author(s): Minasov, G., Shuvalova, L., Hung, D., Fisher, S.L., Edelstein, J., Kiryukhina, O., Dubrovska, I., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.178 (DCC)
R-Value Observed:
0.175 (Depositor)

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

2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from Mycobacterium smegmatis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine.

Minasov, G., Shuvalova, L., Hung, D., Fisher, S.L., Edelstein, J., Kiryukhina, O., Dubrovska, I., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 284.95 kDa
Atom Count: 20,342
Modeled Residue Count: 2,443
Deposited Residue Count: 2,600
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA synthase	A, B, C, D	650	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: fadD32, MSMEG_6393, MSMEI_6225 EC: 6.2.1.20
UniProt
Find proteins for A0R618 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R618 Go to UniProtKB: A0R618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0R618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
649 Query on 649 Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine C₂₇ H₃₈ N₆ O₈ S VLRIGNDIFPKPGQ-ZCIWVVNKSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth B], L [auth C], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.173 (Depositor), 0.178 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.294	α = 90
b = 153.561	β = 90
c = 201.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description