3NM9 | pdb_00003nm9

HMGD(M13A)-DNA complex

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 [auth P]	d3nm9p_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
E [auth M]	d3nm9m_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
D [auth J]	d3nm9j_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C [auth G]	d3nm9g_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B [auth D]	d3nm9d_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d3nm9a_	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth P]	SCOP2B Superfamily	HMG-box	8036769	3001368	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	HMG-box	8036769	3001368	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	HMG-box	8036769	3001368	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	HMG-box	8036769	3001368	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	HMG-box	8036769	3001368	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HMG-box	8036769	3001368	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 [auth P]		e3nm9P1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (develop294)
E [auth M]		e3nm9M1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (develop294)
D [auth J]		e3nm9J1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (develop294)
C [auth G]		e3nm9G1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (develop294)
B [auth D]		e3nm9D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (develop294)
A	GatC	e3nm9A1	A: alpha bundles	X: Repetitive alpha hairpins	H: Glu-tRNAGln amidotransferase C subunit	T: Glu-tRNAGln amidotransferase C subunit	F: GatC	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth P]	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
E [auth M]	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
D [auth J]	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
C [auth G]	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
B [auth D]	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)
A	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth B], H [auth C], I [auth E], J [auth F], K [auth H], G [auth B], H [auth C], I [auth E], J [auth F], K [auth H], L [auth I], M [auth K], N [auth L], O [auth N], P [auth O]	DNA 5'-D(GGPCPGPAPTPAPTPCPGP*C)-3'	-	-	-
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	High mobility group protein D	DNA binding binding nucleic acid binding DNA binding, bending DNA secondary structure binding minor groove of adenine-thymine-rich DNA binding	cellular component organization chromatin organization cellular process cellular component organization or biogenesis chromatin remodeling	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	IPR050342	High Mobility Group Box (HMGB)	Family
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	IPR009071	High mobility group box domain	Domain
A, B [auth D], C [auth G], D [auth J], E [auth M], A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	IPR036910	High mobility group box 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.