3QSI | pdb_00003qsi

Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy

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)
D [auth A]	d3qsia_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
J [auth I]	d3qsii_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
I [auth J]	d3qsij_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
H [auth E]	d3qsie_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
G [auth H]	d3qsih_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
F [auth G]	d3qsig_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
E [auth F]	d3qsif_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
C [auth D]	d3qsid_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
B [auth C]	d3qsic_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)
A [auth B]	d3qsib_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori ) [TaxId: 210 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
H [auth E]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	ACT-like	8074828	3000006	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)
D [auth A]	NikR_C	e3qsiA1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
J [auth I]	NikR_C	e3qsiI1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
I [auth J]	NikR_C	e3qsiJ1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
H [auth E]	NikR_C	e3qsiE1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
G [auth H]	NikR_C	e3qsiH1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
F [auth G]	NikR_C	e3qsiG1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
E [auth F]	NikR_C	e3qsiF1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
C [auth D]	NikR_C	e3qsiD1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
B [auth C]	NikR_C	e3qsiC1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)
A [auth B]	NikR_C	e3qsiB1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: NikR_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
J [auth I]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
I [auth J]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
H [auth E]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
G [auth H]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
F [auth G]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
E [auth F]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
C [auth D]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
B [auth C]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
A [auth B]	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	PF08753	NikR C terminal nickel binding domain (NikR_C)	NikR C terminal nickel binding domain	NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains fou ...	NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	NikR nickel-responsive regulator	DNA binding binding nucleic acid binding cation binding transition metal ion binding ion binding nickel cation binding metal ion binding small molecule binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding DNA binding binding nucleic acid binding cation binding transition metal ion binding ion binding nickel cation binding metal ion binding small molecule binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding identical protein binding protein binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to stimulus response to metal ion response to chemical response to nickel cation	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR022988	Nickel-responsive transcriptional regulator NikR	Family
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR027271	Acetolactate synthase/Transcription factor NikR, C-terminal	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR045865	ACT-like domain	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR014864	Transcription factor, NikR, nickel binding C-terminal	Domain
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR002145	Ribbon-helix-helix protein, CopG	Domain
A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth G], G [auth H], H [auth E], I [auth J], J [auth I]	IPR050192	Nickel-responsive transcriptional regulator	Family

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.