5H9T

Crystal structure of native NalD at resolution of 2.9, the secondary repressor of MexAB-OprM multidrug efflux pump in Pseudomonas aeruginosa

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Homeodomain-like	8090163	3000001	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	TetR C-terminal domain-like	8090164	3000086	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	TetR_N	e5h9tA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
A	TetR_C_2	e5h9tA1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
B	TetR_N	e5h9tB2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
B	TetR_C_2	e5h9tB1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
C	TetR_N	e5h9tC2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
C	TetR_C_2	e5h9tC1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
D	TetR_N	e5h9tD1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
D	TetR_C_2	e5h9tD2	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
E	TetR_N	e5h9tE1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
E	TetR_C_2	e5h9tE2	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
F	TetR_N	e5h9tF2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
F	TetR_C_2	e5h9tF1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
G	TetR_N	e5h9tG2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
G	TetR_C_2	e5h9tG1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)
H	TetR_N	e5h9tH2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: TetR_N	ECOD (1.6)
H	TetR_C_2	e5h9tH1	A: alpha bundles	X: Tetracyclin repressor-like, C-terminal domain (From Topology)	H: Tetracyclin repressor-like, C-terminal domain (From Topology)	T: Tetracyclin repressor-like, C-terminal domain	F: TetR_C_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
B	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
C	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
D	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
E	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
F	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
G	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
H	1.10.357.10	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	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	PF08361	MAATS-type transcriptional repressor, C-terminal region (TetR_C_2)	MAATS-type transcriptional repressor, C-terminal region	This domain is named after the various transcriptional regulatory proteins that it contains, including MtrR (Swiss:Q6RV06), AcrR (Swiss:P34000), ArpR (Swiss:Q9KJC4), TtgR (Swiss:Q9AIU0) and SmeT (Swiss:Q8KLP4). These are members of the TetR family of ...	This domain is named after the various transcriptional regulatory proteins that it contains, including MtrR (Swiss:Q6RV06), AcrR (Swiss:P34000), ArpR (Swiss:Q9KJC4), TtgR (Swiss:Q9AIU0) and SmeT (Swiss:Q8KLP4). These are members of the TetR family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins [1,2,3]. This domain binds multiple drugs, antibiotics, flavonoids and indole (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF00440	Bacterial regulatory proteins, tetR family (TetR_N)	Bacterial regulatory proteins, tetR family	-	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	NalD	DNA binding binding organic cyclic compound binding nucleic acid 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 transcription regulator activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process regulation of localization localization regulation of transport transport negative regulation of transport establishment of localization negative regulation of transmembrane transport transmembrane transport regulation of transmembrane transport	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023772	DNA-binding HTH domain, TetR-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001647	DNA-binding HTH domain, TetR-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013572	Transcription regulator MAATS, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036271	Tetracyclin repressor-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily

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.