1NMO | pdb_00001nmo

Structural genomics, protein ybgI, unknown function

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d1nmof_	Alpha and beta proteins (a/b)	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	Hypothetical protein YbgI	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
E	d1nmoe_	Alpha and beta proteins (a/b)	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	Hypothetical protein YbgI	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
D	d1nmod_	Alpha and beta proteins (a/b)	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	Hypothetical protein YbgI	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
C	d1nmoc_	Alpha and beta proteins (a/b)	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	Hypothetical protein YbgI	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
B	d1nmob_	Alpha and beta proteins (a/b)	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	Hypothetical protein YbgI	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)
A	d1nmoa_	Alpha and beta proteins (a/b)	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	NIF3 (NGG1p interacting factor 3)-like	Hypothetical protein YbgI	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli O157:H7 ) [TaxId: 83334 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	NIF3-like	8036937	3001101	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	NIF3-like	8036937	3001101	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NIF3-like	8036937	3001101	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NIF3-like	8036937	3001101	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NIF3-like	8036937	3001101	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NIF3-like	8036937	3001101	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)
F	DUF34_NIF3	e1nmoF1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
E	DUF34_NIF3	e1nmoE1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
D	DUF34_NIF3	e1nmoD1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
C	DUF34_NIF3	e1nmoC1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
B	DUF34_NIF3	e1nmoB1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)
A	DUF34_NIF3	e1nmoA1	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: DUF34_NIF3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.1390.30	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
E	3.40.1390.30	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
D	3.40.1390.30	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
C	3.40.1390.30	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
B	3.40.1390.30	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	CATH (4.3.0)
A	3.40.1390.30	Alpha Beta	3-Layer(aba) Sandwich	Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase	Chain: A, domain 1	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	PF01784	Duf34/NIF3 (NGG1p interacting factor 3) (DUF34_NIF3)	Duf34/NIF3 (NGG1p interacting factor 3)	-	Family

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	Hypothetical protein ybgI	cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus cellular response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus cellular response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell pole

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR002678	DUF34/NIF3	Family
A, B, C, D, E A, B, C, D, E, F	IPR036069	DUF34/NIF3 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.