3P1M

Crystal structure of human ferredoxin-1 (FDX1) in complex with iron-sulfur cluster

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3p1ma1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3p1ma2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3p1mb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3p1mb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3p1mc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3p1mc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3p1md1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3p1md2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3p1me1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3p1me2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3p1mf1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3p1mf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3p1mg1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d3p1mg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3p1mh1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d3p1mh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2B (2022-06-29)
F	SCOP2 Family	2Fe-2S ferredoxin-related	8068752	4000982	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8068753	3000113	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	Fer2	e3p1mA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
B	Fer2	e3p1mB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
C	Fer2	e3p1mC2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
D	Fer2	e3p1mD2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
E	Fer2	e3p1mE2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
F	Fer2	e3p1mF2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
G	Fer2	e3p1mG2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)
H	Fer2	e3p1mH2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
C	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
D	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
E	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
F	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
G	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
H	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00111	2Fe-2S iron-sulfur cluster binding domain (Fer2)	2Fe-2S iron-sulfur cluster binding domain	-	Domain

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, G, H	Adrenodoxin, mitochondrial	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding electron transfer activity	cellular metabolic process electron transport chain metabolic process cellular process generation of precursor metabolites and energy biosynthetic process regulation of hormone levels biological regulation regulation of biological quality hormone biosynthetic process hormone metabolic process steroid metabolic process lipid biosynthetic process primary metabolic process cellular metabolic process electron transport chain metabolic process cellular process generation of precursor metabolites and energy biosynthetic process regulation of hormone levels biological regulation regulation of biological quality hormone biosynthetic process hormone metabolic process steroid metabolic process lipid biosynthetic process primary metabolic process organic cyclic compound metabolic process organic substance metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process steroid biosynthetic process lipid metabolic process P450-containing electron transport chain organic hydroxy compound metabolic process sterol metabolic process cholesterol metabolic process alcohol metabolic process secondary alcohol metabolic process small molecule metabolic process cellular response to stimulus cellular response to nitrogen compound response to organic substance response to stimulus response to organonitrogen compound response to endogenous stimulus response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular response to cAMP cellular response to organic substance response to organic cyclic compound response to ketone response to lipid response to alcohol cellular response to forskolin cellular response to alcohol response to forskolin cellular response to lipid cellular response to ketone	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001055	Adrenodoxin-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018298	Adrenodoxin, iron-sulphur binding site	Binding Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: P10109	adrenal cortex carcinoma ovarian cancer ulcerative colitis heart disease pancreatic ductal adenocarcinoma myocardial infarction plasma cell myeloma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.