4X3F | pdb_00004x3f

Crystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA

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
Protein Modification Annotation

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)	8083902	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8083902	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8083902	3000066	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	Pkinase_Tyr	e4x3fA1	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: Pkinase_Tyr	ECOD (1.6)
B	Pkinase_Tyr	e4x3fB1	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: Pkinase_Tyr	ECOD (1.6)
C	Pkinase_Tyr	e4x3fC1	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: Pkinase_Tyr	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 (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
B	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
C	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Serine/threonine-protein kinase PknA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity	developmental process regulation of biological process regulation of developmental process biological regulation 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 protein phosphorylation protein autophosphorylation phosphorylation developmental process regulation of biological process regulation of developmental process biological regulation 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 protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process peptidyl-threonine autophosphorylation macromolecule modification phosphate-containing compound metabolic process peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process peptidyl-threonine modification protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic 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 regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process fatty acid metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process carboxylic acid metabolic process organic acid metabolic process regulation of ketone metabolic process regulation of small molecule metabolic process regulation of fatty acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process lipid metabolic process negative regulation of metabolic process negative regulation of biological process lipid biosynthetic process negative regulation of lipid biosynthetic process negative regulation of biosynthetic process negative regulation of cellular process regulation of lipid biosynthetic process negative regulation of lipid metabolic process negative regulation of small molecule metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process negative regulation of fatty acid biosynthetic process negative regulation of fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process fatty acid biosynthetic process regulation of fatty acid biosynthetic process	cellular anatomical structure extracellular region intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane
B	Serine/threonine-protein kinase PknA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity	developmental process regulation of biological process regulation of developmental process biological regulation 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 protein phosphorylation protein autophosphorylation phosphorylation developmental process regulation of biological process regulation of developmental process biological regulation 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 protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process peptidyl-threonine autophosphorylation macromolecule modification phosphate-containing compound metabolic process peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process peptidyl-threonine modification protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic 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 regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process fatty acid metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process carboxylic acid metabolic process organic acid metabolic process regulation of ketone metabolic process regulation of small molecule metabolic process regulation of fatty acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process lipid metabolic process negative regulation of metabolic process negative regulation of biological process lipid biosynthetic process negative regulation of lipid biosynthetic process negative regulation of biosynthetic process negative regulation of cellular process regulation of lipid biosynthetic process negative regulation of lipid metabolic process negative regulation of small molecule metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process negative regulation of fatty acid biosynthetic process negative regulation of fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process fatty acid biosynthetic process regulation of fatty acid biosynthetic process	cellular anatomical structure extracellular region intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane
C	Serine/threonine-protein kinase PknA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity	developmental process regulation of biological process regulation of developmental process biological regulation 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 protein phosphorylation protein autophosphorylation phosphorylation developmental process regulation of biological process regulation of developmental process biological regulation 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 protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process peptidyl-threonine autophosphorylation macromolecule modification phosphate-containing compound metabolic process peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process peptidyl-threonine modification protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic 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 regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process fatty acid metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process carboxylic acid metabolic process organic acid metabolic process regulation of ketone metabolic process regulation of small molecule metabolic process regulation of fatty acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process lipid metabolic process negative regulation of metabolic process negative regulation of biological process lipid biosynthetic process negative regulation of lipid biosynthetic process negative regulation of biosynthetic process negative regulation of cellular process regulation of lipid biosynthetic process negative regulation of lipid metabolic process negative regulation of small molecule metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process negative regulation of fatty acid biosynthetic process negative regulation of fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process fatty acid biosynthetic process regulation of fatty acid biosynthetic process	cellular anatomical structure extracellular region intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR000719	Protein kinase domain	Domain
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR000719	Protein kinase domain	Domain
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site
C	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C	IPR000719	Protein kinase domain	Domain
C	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047
B	TPO	Parent Component: THR RESID: AA0037 , AA0038 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047 , O-phospho-L-threonine MOD:00047
C	TPO	Parent Component: THR RESID: AA0037 , AA0038 , AA0038 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047 , O-phospho-L-threonine MOD:00047 , O-phospho-L-threonine MOD:00047

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.