7RK3 | pdb_00007rk3

Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8032317	3000403	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8032315	3000403	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	RF-1	e7rk3A1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: RF-1	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02799	Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain (NMT_C)	Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain	The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	ADP-ribosylation factor 6	thioesterase binding protein binding binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity thioesterase binding protein binding binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding G protein activity molecular function regulator activity	regulation of localization regulation of biological process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface macromolecule localization regulation of protein localization to cell surface intracellular protein localization negative regulation of protein localization cellular response to stimulus regulation of signaling regulation of localization regulation of biological process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface macromolecule localization regulation of protein localization to cell surface intracellular protein localization negative regulation of protein localization cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication cellular process signal transduction cell division positive regulation of protein localization to plasma membrane cellular localization positive regulation of biological process regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization positive regulation of protein localization regulation of protein localization to plasma membrane establishment of cell polarity establishment of epithelial cell polarity establishment or maintenance of cell polarity regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of developmental process nervous system development negative regulation of neuron projection development negative regulation of dendrite development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor protein localization to cleavage furrow protein localization to cell division site positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization import into cell transport negative regulation of transport negative regulation of endocytosis vesicle-mediated transport regulation of endocytosis negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis regulation of dendritic spine development dendritic spine development organelle organization actin cytoskeleton organization cortical actin cytoskeleton organization cortical cytoskeleton organization actin filament-based process cytoskeleton organization positive regulation of locomotion regulation of cell motility regulation of keratinocyte migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion positive regulation of keratinocyte migration keratinocyte migration cell adhesion cellular component disassembly regulation of focal adhesion disassembly focal adhesion disassembly cell junction disassembly cell-substrate junction disassembly positive regulation of cell-substrate junction organization cell junction organization positive regulation of focal adhesion disassembly cell-substrate junction organization regulation of cell-substrate junction organization hepaticobiliary system development gland development animal organ development liver development maintenance of synapse structure postsynapse organization cellular component maintenance maintenance of postsynaptic density structure cell junction maintenance maintenance of postsynaptic specialization structure postsynaptic density organization synapse organization postsynaptic specialization organization synaptic vesicle endocytosis synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell protein localization to endosome protein localization to organelle regulation of presynapse assembly cellular component biogenesis cellular component assembly regulation of presynapse organization cell junction assembly regulation of synapse structure or activity regulation of synapse assembly regulation of biological quality presynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization synapse assembly presynapse assembly positive regulation of cell division cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis mitotic cytokinetic process mitotic cytokinesis mitotic cell cycle regulation of cell division regulation of mitotic cytokinesis positive regulation of cytokinesis positive regulation of mitotic cytokinetic process positive regulation of cell cycle process cell cycle regulation of cell cycle cell cycle process regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cytokinetic process positive regulation of cell cycle mitotic cell cycle process cytokinetic process establishment of protein localization intracellular transport protein transport intracellular protein transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell positive regulation of secretion secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport myeloid cell apoptotic process erythrocyte apoptotic process apoptotic process cell death programmed cell death ruffle organization plasma membrane bounded cell projection assembly ruffle assembly cell projection assembly hepatocyte apoptotic process epithelial cell apoptotic process positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization protein-containing complex assembly regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization regulation of anatomical structure size filopodium assembly regulation of cell projection assembly regulation of filopodium assembly regulation of plasma membrane bounded cell projection assembly endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle endocytic vesicle synapse cell junction glutamatergic synapse Golgi apparatus endomembrane system ruffle cell projection cell leading edge plasma membrane bounded cell projection postsynapse midbody anchoring junction focal adhesion cell-substrate junction cell periphery cell cortex plasma membrane presynapse cell division site cleavage furrow plasma membrane region endosome membrane endosome recycling endosome cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane organelle membrane early endosome early endosome membrane Flemming body filopodium membrane actin-based cell projection filopodium cell projection membrane
A	Glycylpeptide N-tetradecanoyltransferase 1	myristoyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity catalytic activity, acting on a protein peptidyl-lysine N6-myristoyltransferase activity glycylpeptide N-tetradecanoyltransferase activity N-acyltransferase activity	regulation of localization regulation of biological process regulation of protein localization biological regulation positive regulation of biological process regulation of protein localization to mitochondrion localization macromolecule localization protein localization to organelle positive regulation of protein localization protein localization to mitochondrion intracellular protein localization positive regulation of protein localization to mitochondrion lipoprotein biosynthetic process regulation of localization regulation of biological process regulation of protein localization biological regulation positive regulation of biological process regulation of protein localization to mitochondrion localization macromolecule localization protein localization to organelle positive regulation of protein localization protein localization to mitochondrion intracellular protein localization positive regulation of protein localization to mitochondrion lipoprotein biosynthetic process lipoprotein metabolic process primary metabolic process N-terminal protein lipidation macromolecule biosynthetic process N-terminal protein myristoylation protein acylation protein lipidation biosynthetic process protein myristoylation N-terminal protein amino acid modification peptidyl-glycine modification macromolecule modification peptidyl-amino acid modification metabolic process cellular process N-terminal peptidyl-glycine N-myristoylation protein metabolic process macromolecule metabolic process protein modification process ketone metabolic process cellular localization localization within membrane protein localization to membrane cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus regulation of response to external stimulus signaling regulation of opsin-mediated signaling pathway regulation of signal transduction detection of abiotic stimulus cellular response to environmental stimulus cell communication cellular response to light stimulus signal transduction regulation of G protein-coupled receptor signaling pathway detection of light stimulus phototransduction detection of external stimulus regulation of signaling detection of visible light response to external stimulus cellular response to radiation detection of stimulus regulation of response to stimulus regulation of cell communication response to radiation response to abiotic stimulus G protein-coupled receptor signaling pathway cellular response to abiotic stimulus G protein-coupled opsin signaling pathway phototransduction, visible light developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
B	IPR041838	ADP-ribosylation factor 6	Family
B	IPR005225	Small GTP-binding domain	Domain
B	IPR024156	Small GTPase superfamily, ARF type	Family
A	IPR022676	Glycylpeptide N-tetradecanoyltransferase, N-terminal	Domain
A	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
A	IPR022677	Glycylpeptide N-tetradecanoyltransferase, C-terminal	Domain
A	IPR000903	Glycylpeptide N-tetradecanoyltransferase	Family
A	IPR022678	Glycylpeptide N-tetradecanoyltransferase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P62330	astrocytic tumor juvenile dermatomyositis osteosarcoma psoriasis esophageal adenocarcinoma malignant pancreatic neoplasm ovarian cancer glioblastoma myopathy pancreatic intraductal papillary-mucinous neoplasm
A	Pharos: P30419	astrocytic tumor glioblastoma malignant glioma ovarian cancer atypical teratoid rhabdoid tumor hypertensive disorder medulloblastoma primitive neuroectodermal tumor dermatomyositis lung cancer osteosarcoma psoriasis

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.