5USR | pdb_00005usr

Crystal structure of human NFS1-ISD11 in complex with E. coli acyl-carrier protein at 3.09 angstroms

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I	d5usri_	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
K	d5usrk_	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
L	d5usrl_	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
J	d5usrj_	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d5usrb_	Membrane and cell surface proteins and peptides	LYR proteins from mammalian respiratory complex I	LYR protein-like	LYR proteins	LYR motif-containing protein 4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5usrf_	Membrane and cell surface proteins and peptides	LYR proteins from mammalian respiratory complex I	LYR protein-like	LYR proteins	LYR motif-containing protein 4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5usrh_	Membrane and cell surface proteins and peptides	LYR proteins from mammalian respiratory complex I	LYR protein-like	LYR proteins	LYR motif-containing protein 4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5usrd_	Membrane and cell surface proteins and peptides	LYR proteins from mammalian respiratory complex I	LYR protein-like	LYR proteins	LYR motif-containing protein 4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5usrc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5usre1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5usre2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5usrg1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5usrg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5usra1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5usra2	Artifacts	Tags	Tags	Tags	N-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)
I	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	ACP-like	8040084	3001805	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8074674	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8074674	3000954	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)
I		e5usrI1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
K		e5usrK1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
L		e5usrL1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
J		e5usrJ1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
B		e5usrB1	A: Four-helical up-and-down bundle	X: RelE-like	H: RelE-like	T:	F:	ECOD (20:10:01)
F		e5usrF1	A: Four-helical up-and-down bundle	X: RelE-like	H: RelE-like	T:	F:	ECOD (20:10:01)
H		e5usrH1	A: Four-helical up-and-down bundle	X: RelE-like	H: RelE-like	T:	F:	ECOD (20:10:01)
D		e5usrD1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
C		e5usrC1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
E		e5usrE2	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
E		e5usrE3	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T: IDH	F:	ECOD (20:10:01)
G		e5usrG1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)
A		e5usrA1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: ANAPC3, SRP_TPR_like	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
G	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I, J, K, L	PF00550	Phosphopantetheine attachment site (PP-binding)	Phosphopantetheine attachment site	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.	Domain
B, D, F, H	PF05347	Complex 1 protein (LYR family) (Complex1_LYR)	Complex 1 protein (LYR family)	-	Family
A, C, E, G	PF00266	Aminotransferase class-V (Aminotran_5)	Aminotransferase class-V	This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L	Acyl carrier protein	phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding lipid binding vitamin binding modified amino acid binding ion binding anion binding phosphopantetheine binding sulfur compound binding small molecule binding phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding lipid binding vitamin binding modified amino acid binding ion binding anion binding phosphopantetheine binding sulfur compound binding small molecule binding acyl binding	response to stimulus response to chemical response to xenobiotic stimulus 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 response to stimulus response to chemical response to xenobiotic stimulus 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 cytosol
B, D, F, H	LYR motif-containing protein 4	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity molecular adaptor activity structural molecule activity	cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis [2Fe-2S] cluster assembly [4Fe-4S] cluster assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex L-cysteine desulfurase complex cytosol mitochondrial [2Fe-2S] assembly complex nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear body nucleoplasm organelle lumen membraneless organelle nuclear lumen mitochondrial matrix
A, C, E, G	Cysteine desulfurase, mitochondrial	cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding cysteine desulfurase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding sulfur carrier activity molecular carrier activity identical protein binding protein binding protein homodimerization activity protein dimerization activity cation binding metal ion binding	cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis [4Fe-4S] cluster assembly Mo-molybdopterin cofactor biosynthetic process Mo-molybdopterin cofactor metabolic process primary metabolic process prosthetic group metabolic process molybdopterin cofactor biosynthetic process biosynthetic process cellular component biogenesis cellular component organization metallo-sulfur cluster assembly cellular component assembly iron-sulfur cluster assembly cellular process cellular component organization or biogenesis [4Fe-4S] cluster assembly Mo-molybdopterin cofactor biosynthetic process Mo-molybdopterin cofactor metabolic process primary metabolic process prosthetic group metabolic process molybdopterin cofactor biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process molybdopterin cofactor metabolic process phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process phosphorus metabolic process [2Fe-2S] cluster assembly	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex iron-sulfur cluster assembly complex mitochondrial protein-containing complex catalytic complex sulfurtransferase complex transferase complex L-cysteine desulfurase complex cytosol mitochondrial [2Fe-2S] assembly complex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I, J, K, L	IPR006162	Phosphopantetheine attachment site	PTM
I, J, K, L	IPR009081	Phosphopantetheine binding ACP domain	Domain
I, J, K, L	IPR036736	ACP-like superfamily	Homologous Superfamily
I, J, K, L	IPR003231	Acyl carrier protein	Family
B, D, F, H	IPR051522	Iron-sulfur cluster assembly LYR protein	Family
B, D, F, H	IPR008011	Complex 1 LYR protein domain	Domain
B, D, F, H	IPR045297	LYRM4, LYR domain	Domain
A, C, E, G	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A, C, E, G	IPR000192	Aminotransferase class V domain	Domain
A, C, E, G	IPR010240	Cysteine desulfurase IscS	Family
A, C, E, G	IPR016454	Cysteine desulfurase	Family
A, C, E, G	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, C, E, G	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, C, E, G	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: Q9HD34	combined oxidative phosphorylation deficiency 19 breast cancer Friedreich ataxia Mitochondrial Diseases pancreatic intraductal papillary-mucinous neoplasm squamous cell carcinoma combined oxidative phosphorylation deficiency lung cancer osteosarcoma schizophrenia medulloblastoma ovarian cancer skin basal cell carcinoma
A, C, E, G	Pharos: Q9Y697	Friedreich ataxia Mitochondrial Diseases skin carcinoma large cell medulloblastoma osteosarcoma medulloblastoma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E, G	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.