6I2P

Crystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in complex with its substrate GarA

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6i2pa_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d6i2pb_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D [auth E]	d6i2pe_	All beta proteins	SMAD/FHA domain	SMAD/FHA domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8044066	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8044066	3000066	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	SMAD/FHA domain-like	8103785	3000137	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	SMAD/FHA domain-like	8103785	3000137	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	PF00069	e6i2pA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PF00069	ECOD (1.6)
B	PF00069	e6i2pB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PF00069	ECOD (1.6)
C [auth D]	PF00498	e6i2pD1	A: beta sandwiches	X: SMAD/FHA domain (From Topology)	H: SMAD/FHA domain (From Topology)	T: SMAD/FHA domain	F: PF00498	ECOD (1.6)
D [auth E]	PF00498	e6i2pE1	A: beta sandwiches	X: SMAD/FHA domain (From Topology)	H: SMAD/FHA domain (From Topology)	T: SMAD/FHA domain	F: PF00498	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (utative)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (utative)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (utative)
C [auth D]	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (utative)
D [auth E]	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
C [auth D], D [auth E]	PF00498	FHA domain (FHA)	FHA domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Serine/threonine-protein kinase PknB	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding enzyme regulator activity enzyme activator activity molecular function activator activity acetyltransferase activator activity molecular function regulator activity protein serine/threonine kinase activity identical protein binding protein binding	regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding regulation of protein binding negative regulation of protein binding negative regulation of binding negative regulation of molecular function response to host defenses biological process involved in interspecies interaction between organisms response to stimulus regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding regulation of protein binding negative regulation of protein binding negative regulation of binding negative regulation of molecular function response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to defenses of other organism response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction response to host immune response response to host response to external biotic stimulus regulation of biological process regulation of growth negative regulation of growth negative regulation of growth rate negative regulation of biological process growth regulation of growth rate cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis organic substance metabolic process peptidoglycan metabolic process organic substance biosynthetic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis organonitrogen compound metabolic process cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process macromolecule metabolic process protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process developmental process regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis regulation of catalytic activity negative regulation of catalytic activity positive regulation of catalytic activity regulation of cellular process negative regulation of small molecule metabolic process oxoacid metabolic process regulation of lipid metabolic process organic acid metabolic process organic acid biosynthetic process negative regulation of lipid biosynthetic process negative regulation of cellular metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process cellular ketone metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of cellular ketone metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process cellular lipid metabolic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process negative regulation of lipid metabolic process lipid biosynthetic process negative regulation of cellular process negative regulation of fatty acid biosynthetic process regulation of biosynthetic process fatty acid metabolic process negative regulation of fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process regulation of lipid biosynthetic process lipid metabolic process	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall
C [auth D], D [auth E]	Glycogen accumulation regulator GarA	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding identical protein binding protein binding molecular function inhibitor activity molecular function regulator activity	pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process regulation of small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process regulation of small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process negative regulation of carbohydrate metabolic process nucleoside phosphate metabolic process organonitrogen compound catabolic process pyruvate metabolic process cellular metabolic process negative regulation of metabolic process negative regulation of purine nucleotide catabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process metabolic process regulation of phosphorus metabolic process monocarboxylic acid metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process ATP metabolic process negative regulation of purine nucleotide metabolic process negative regulation of phosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process negative regulation of nucleotide catabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process organic cyclic compound catabolic process purine-containing compound metabolic process ADP metabolic process negative regulation of phosphorus metabolic process purine ribonucleoside diphosphate metabolic process cellular process organic substance catabolic process purine ribonucleoside diphosphate catabolic process ribonucleotide catabolic process regulation of cellular process negative regulation of small molecule metabolic process negative regulation of glycolytic process negative regulation of biological process negative regulation of ATP metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process glycolytic process pyridine-containing compound metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nicotinamide nucleotide metabolic process regulation of carbohydrate catabolic process regulation of biological process regulation of cellular metabolic process nucleotide metabolic process organic cyclic compound metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process regulation of metabolic process catabolic process organic substance metabolic process purine nucleotide metabolic process ribonucleotide metabolic process negative regulation of cellular process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process ribonucleoside triphosphate metabolic process negative regulation of catabolic process purine nucleoside triphosphate metabolic process carbohydrate metabolic process organonitrogen compound metabolic process biological regulation ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process organophosphate metabolic process cellular respiration energy derivation by oxidation of organic compounds regulation of cellular respiration protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification protein metabolic process macromolecule metabolic process protein modification process	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall extracellular region
E [auth C]	UNK-UNK-UNK-UNK-UNK	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR005543	PASTA domain	Domain
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR008271	Serine/threonine-protein kinase, active site	Active Site
C [auth D], D [auth E]	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR000253	Forkhead-associated (FHA) domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047
E [auth C]	UNK	RESID: AA0038

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.