3LAP | pdb_00003lap

The Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-canavanine.

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)
F	SCOP2B Superfamily	ArgR regulatory domain-like	8064286	3000096	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ArgR regulatory domain-like	8064286	3000096	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ArgR regulatory domain-like	8064286	3000096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ArgR regulatory domain-like	8064286	3000096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ArgR regulatory domain-like	8064286	3000096	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ArgR regulatory domain-like	8064286	3000096	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		e3lapF5	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
E		e3lapE5	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
D		e3lapD5	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
C		e3lapC3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Acetyltransf_1	F:	ECOD (20:10:01)
B		e3lapB3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Acetyltransf_1	F:	ECOD (20:10:01)
A		e3lapA3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Acetyltransf_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
F	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	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	PF01316	Arginine repressor, DNA binding domain (Arg_repressor)	Arginine repressor, DNA binding domain		Domain
A, B, C, D, E A, B, C, D, E, F	PF02863	Arginine repressor, C-terminal domain (Arg_repressor_C)	Arginine repressor, C-terminal domain	This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization [1,2]. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.o ...	This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization [1,2]. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H, J, L	5'-D(TPTPGPCPAPTPCPGPTPTPAPTPGPCPAPA)-3'	-	-	-
G, I, K	5'-D(TPTPGPCPAPTPAPAPCPGPAPTPGPCPAPA)-3'	-	-	-
A, B, C, D, E A, B, C, D, E, F	Arginine repressor	DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity cation binding organic acid binding ion binding DNA binding binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity cation binding organic acid binding ion binding anion binding amino acid binding carboxylic acid binding arginine binding small molecule binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process arginine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process small molecule metabolic process alpha-amino acid biosynthetic process regulation of cellular process regulation of arginine biosynthetic process regulation of amino acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of amino acid metabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of metabolic process	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001669	Arginine repressor	Family
A, B, C, D, E A, B, C, D, E, F	IPR020899	Arginine repressor, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR020900	Arginine repressor, DNA-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036251	Arginine repressor, C-terminal 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.