3D04 | pdb_00003d04

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3d04a_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	FabZ-like	(3R)-hydroxymyristoyl ACP dehydrase FabZ	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
B	d3d04b_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	FabZ-like	(3R)-hydroxymyristoyl ACP dehydrase FabZ	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C	d3d04c_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	FabZ-like	(3R)-hydroxymyristoyl ACP dehydrase FabZ	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
D	d3d04d_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	FabZ-like	(3R)-hydroxymyristoyl ACP dehydrase FabZ	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
E	d3d04e_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	FabZ-like	(3R)-hydroxymyristoyl ACP dehydrase FabZ	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
F	d3d04f_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	FabZ-like	(3R)-hydroxymyristoyl ACP dehydrase FabZ	(Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8088180	3000149	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8088180	3000149	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8088180	3000149	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8088180	3000149	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8088180	3000149	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8088180	3000149	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	IL7	e3d04A1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
B	IL7	e3d04B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
C	IL7	e3d04C1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
D	IL7	e3d04D1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
E	IL7	e3d04E1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
F	IL7	e3d04F1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
B	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
C	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
D	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
E	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
F	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	(3R)-hydroxymyristoyl-acyl carrier protein dehydratase	(3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic process carbohydrate derivative biosynthetic process lipooligosaccharide metabolic process glycolipid metabolic process lipid A biosynthetic process liposaccharide metabolic process carbohydrate derivative metabolic process glycolipid biosynthetic process phospholipid biosynthetic process phospholipid metabolic process lipid A metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process lipooligosaccharide biosynthetic process phosphorus metabolic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR010084	Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ	Family
A, B, C, D, E A, B, C, D, E, F	IPR013114	Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ	Family
A, B, C, D, E A, B, C, D, E, F	IPR029069	HotDog domain superfamily	Homologous Superfamily

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.