6ARE | pdb_00006are

Aspergillus fumigatus Cytosolic Thiolase in complex with two tetrahedral reaction intermediates and ammonium ions

PDB DOI: https://doi.org/10.2210/pdb6ARE/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-22 Released: 2018-05-30
Deposition Author(s): Marshall, A.C., Bond, C.S., Bruning, J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.232 (Depositor), 0.233 (DCC)
R-Value Work:
0.194 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations

Marshall, A.C., Bond, C.S., Bruning, J.B.

(2018) ACS Catal 8(3): 1973-1989

DOI: https://doi.org/10.1021/acscatal.7b02873

Macromolecule Content

Total Structure Weight: 167.67 kDa
Atom Count: 13,043
Modeled Residue Count: 1,588
Deposited Residue Count: 1,596
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase, acetylated enzyme	A, B	399	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_8G04000 EC: 2.3.1.9
UniProt
Find proteins for Q4WCL5 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WCL5 Go to UniProtKB: Q4WCL5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WCL5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	C, D	399	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_8G04000 EC: 2.3.1.9
UniProt
Find proteins for Q4WCL5 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WCL5 Go to UniProtKB: Q4WCL5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WCL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C] mmCIF format, chain S [auth C]	S [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain T [auth D] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain I [auth B]	E [auth A], I [auth B], T [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain T [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain U [auth D] MOL2 format, chain N [auth C] MOL2 format, chain U [auth D] mmCIF format, chain N [auth C] mmCIF format, chain U [auth D]	N [auth C], U [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain N [auth C] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain V [auth D]	F [auth A], J [auth B], O [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain V [auth D]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] M [auth B] G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C], W [auth D], X [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY Query on SCY	A, B	L-PEPTIDE LINKING	C₅ H₉ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.232 (Depositor), 0.233 (DCC)
R-Value Work: 0.194 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.36	α = 90
b = 106.59	β = 104.27
c = 110.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data collection
Aimless	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: 2018-05-30

Deposition Author(s):

Marshall, A.C.

Bond, C.S.

Bruning, J.B.

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2025-04-02
Changes: Data collection, Database references, Derived calculations, Structure summary