6DV2 | pdb_00006dv2

Crystal Structure of Human Mitochondrial Trifunctional Protein

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L		e6dv2L1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
K		e6dv2K1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
J		e6dv2J1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
I		e6dv2I1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
H		e6dv2H1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
G		e6dv2G1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Amidohydro_2	F:	ECOD (20:10:01)
B		e6dv2B1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
E		e6dv2E1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
F		e6dv2F1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
D		e6dv2D1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
C		e6dv2C1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: OB_NTP_bind	F:	ECOD (20:10:01)
A		e6dv2A1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Amidohydro_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
K	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
J	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
I	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H, I, J, K G, H, I, J, K, L	PF02737	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain (3HCDH_N)	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain	This family also includes lambda crystallin.	Domain
G, H, I, J, K G, H, I, J, K, L	PF00725	3-hydroxyacyl-CoA dehydrogenase, C-terminal domain (3HCDH)	3-hydroxyacyl-CoA dehydrogenase, C-terminal domain	This family also includes lambda crystallin. Some proteins include two copies of this domain.	Domain
G, H, I, J, K G, H, I, J, K, L	PF00378	Enoyl-CoA hydratase/isomerase (ECH_1)	Enoyl-CoA hydratase/isomerase	This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase.	Domain
A, B, C, D, E A, B, C, D, E, F	PF02803	Thiolase, C-terminal domain (Thiolase_C)	Thiolase, C-terminal domain	Thiolase is reported to be structurally related to beta-ketoacyl synthase (Pfam:PF00109), and also chalcone synthase.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00108	Thiolase, N-terminal domain (Thiolase_N)	Thiolase, N-terminal domain	Thiolase is reported to be structurally related to beta-ketoacyl synthase (Pfam:PF00109), and also chalcone synthase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	Trifunctional enzyme subunit alpha, mitochondrial	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding enoyl-CoA hydratase activity hydro-lyase activity 3-hydroxyacyl-CoA dehydratase activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding enoyl-CoA hydratase activity hydro-lyase activity 3-hydroxyacyl-CoA dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity hydrolase activity, acting on ester bonds thiolester hydrolase activity deacylase activity hydrolase activity fatty acyl-CoA hydrolase activity long-chain fatty acyl-CoA hydrolase activity acyl-CoA hydrolase activity acetyl-CoA C-acetyltransferase activity acetyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity acetyl-CoA C-acyltransferase activity C-acyltransferase activity C-acetyltransferase activity long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	response to stimulus response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process response to stimulus response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process lipid modification organic acid metabolic process organic acid catabolic process fatty acid catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process lipid oxidation small molecule catabolic process lipid metabolic process cardiolipin acyl-chain remodeling phosphatidylglycerol metabolic process glycerophospholipid metabolic process cardiolipin metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerolipid metabolic process phosphorus metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane mitochondrial protein-containing complex protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix intracellular organelle lumen fatty acid beta-oxidation multienzyme complex organelle lumen mitochondrial fatty acid beta-oxidation multienzyme complex oxidoreductase complex intracellular membraneless organelle nucleoid membraneless organelle mitochondrial nucleoid
A, B, C, D, E A, B, C, D, E, F	Trifunctional enzyme subunit beta, mitochondrial	acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity acetyl-CoA C-acyltransferase activity C-acyltransferase activity catalytic activity RNA binding binding lncRNA binding nucleic acid binding acetyl-CoA C-acetyltransferase activity acetyltransferase activity C-acetyltransferase activity enoyl-CoA hydratase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity acetyl-CoA C-acyltransferase activity C-acyltransferase activity catalytic activity RNA binding binding lncRNA binding nucleic acid binding acetyl-CoA C-acetyltransferase activity acetyltransferase activity C-acetyltransferase activity enoyl-CoA hydratase activity hydro-lyase activity lyase activity carbon-oxygen lyase activity myristoyltransferase activity acetyl-CoA C-myristoyltransferase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity protein-containing complex binding	fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process lipid modification organic acid metabolic process organic acid catabolic process fatty acid catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process lipid modification organic acid metabolic process organic acid catabolic process fatty acid catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process lipid oxidation small molecule catabolic process lipid metabolic process cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to stimulus response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin biosynthetic process macromolecule metabolic process gene expression macromolecule biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane cell projection sperm principal piece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial protein-containing complex protein-containing complex catalytic complex transferase complex mitochondrial matrix fatty acid beta-oxidation multienzyme complex mitochondrial fatty acid beta-oxidation multienzyme complex oxidoreductase complex organelle outer membrane bounding membrane of organelle mitochondrial outer membrane outer membrane intracellular membraneless organelle nucleoid membraneless organelle mitochondrial nucleoid endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, J, K G, H, I, J, K, L	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR050136	Fatty acid oxidation complex subunit alpha	Family
G, H, I, J, K G, H, I, J, K, L	IPR018376	Enoyl-CoA hydratase/isomerase, conserved site	Conserved Site
G, H, I, J, K G, H, I, J, K, L	IPR012803	Fatty acid oxidation complex, alpha subunit, mitochondrial	Family
G, H, I, J, K G, H, I, J, K, L	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR006108	3-hydroxyacyl-CoA dehydrogenase, C-terminal	Domain
G, H, I, J, K G, H, I, J, K, L	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR006180	3-hydroxyacyl-CoA dehydrogenase, conserved site	Conserved Site
G, H, I, J, K G, H, I, J, K, L	IPR001753	Enoyl-CoA hydratase/isomerase-like domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002155	Thiolase	Family
A, B, C, D, E A, B, C, D, E, F	IPR020617	Thiolase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020613	Thiolase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR016039	Thiolase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR020616	Thiolase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR020610	Thiolase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR020615	Thiolase, acyl-enzyme intermediate active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G, H, I, J, K G, H, I, J, K, L	Pharos: P40939	long chain 3-hydroxyacyl-CoA dehydrogenase deficiency mitochondrial trifunctional protein deficiency malignant ependymoma oligodendroglioma Osteoarthrosis Deformans pancreatic ductal adenocarcinoma acute fatty liver of pregnancy rheumatoid arthritis astrocytic tumor ulcerative colitis coronary artery disease drug-induced liver injury hydrops fetalis osteoarthritis osteosarcoma long chain 3-hydroxyacyl-CoA dehydrogenase deficiency mitochondrial trifunctional protein deficiency malignant ependymoma oligodendroglioma Osteoarthrosis Deformans pancreatic ductal adenocarcinoma acute fatty liver of pregnancy rheumatoid arthritis astrocytic tumor ulcerative colitis coronary artery disease drug-induced liver injury hydrops fetalis osteoarthritis osteosarcoma plasma cell myeloma adenoma Charcot-Marie-Tooth disease cholestasis malignant colon neoplasm myocardial ischemia osteoarthritis susceptibility 1 ovarian cancer rhabdomyolysis arthrogryposis intellectual disability
A, B, C, D, E A, B, C, D, E, F	Pharos: P55084	mitochondrial trifunctional protein deficiency heart disease breast carcinoma plasma cell myeloma Trifunctional Protein Deficiency With Myopathy And Neuropathy arthrogryposis Charcot-Marie-Tooth disease large cell medulloblastoma lymphoplasmacytic lymphoma ovarian cancer rhabdomyolysis breast cancer medulloblastoma pancreatic ductal adenocarcinoma fatty liver disease mitochondrial trifunctional protein deficiency heart disease breast carcinoma plasma cell myeloma Trifunctional Protein Deficiency With Myopathy And Neuropathy arthrogryposis Charcot-Marie-Tooth disease large cell medulloblastoma lymphoplasmacytic lymphoma ovarian cancer rhabdomyolysis breast cancer medulloblastoma pancreatic ductal adenocarcinoma fatty liver disease inherited lipid metabolism disorder long chain 3-hydroxyacyl-CoA dehydrogenase deficiency

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	Thiolase-like superfamily	Thiolase

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	mpstruc	MONOTOPIC MEMBRANE PROTEINS	Oxidoreductases (Monotopic)	mitochondrial trifunctional protein

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.