3NDP | pdb_00003ndp

Crystal structure of human AK4(L171P)

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3ndpb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ndpb2	Small proteins	Rubredoxin-like	Microbial and mitochondrial ADK, insert 'zinc finger' domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ndpb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ndpa1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ndpa2	Small proteins	Rubredoxin-like	Microbial and mitochondrial ADK, insert 'zinc finger' domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ndpa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058342	3002021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058342	3002021	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)
B	NikR_C	e3ndpB3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: NikR_C	ECOD (v294.1)
A	ADK_lid	e3ndpA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Cu,Zn superoxide dismutase-like	F: ADK_lid	ECOD (v294.1)
A	Sod_Cu	e3ndpA2	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Cu,Zn superoxide dismutase-like	F: Sod_Cu	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00406	Adenylate kinase (ADK)	Adenylate kinase		Domain
A, B	PF05191	Adenylate kinase, active site lid (ADK_lid)	Adenylate kinase, active site lid	Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are resp ...	Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain, is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Adenylate kinase isoenzyme 4	nucleobase-containing compound kinase activity nucleoside monophosphate kinase activity kinase activity AMP kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups deoxynucleoside phosphate kinase activity, ATP as phosphate donor dAMP kinase activity dCMP kinase activity binding guanyl nucleotide binding GTP binding nucleobase-containing compound kinase activity nucleoside monophosphate kinase activity kinase activity AMP kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups deoxynucleoside phosphate kinase activity, ATP as phosphate donor dAMP kinase activity dCMP kinase activity binding 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 adenyl ribonucleotide binding adenyl nucleotide binding ATP binding nucleoside triphosphate adenylate kinase activity CMP kinase activity nucleoside diphosphate kinase activity	ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process nucleoside diphosphate biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process ribonucleoside diphosphate metabolic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process nucleoside diphosphate biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process ribonucleoside diphosphate metabolic process ADP biosynthetic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside diphosphate metabolic process primary metabolic process purine nucleoside diphosphate biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process ADP metabolic process nucleoside diphosphate metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process purine ribonucleoside diphosphate metabolic process metabolic process cellular process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribonucleoside diphosphate biosynthetic process purine nucleoside triphosphate metabolic process ATP metabolic process purine ribonucleoside triphosphate metabolic process nucleoside triphosphate metabolic process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus nucleobase-containing small molecule interconversion aerobic respiration cellular respiration oxidative phosphorylation regulation of biological process regulation of cellular process energy derivation by oxidation of organic compounds biological regulation regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration regulation of oxidative phosphorylation regulation of metabolic process AMP metabolic process purine ribonucleoside monophosphate metabolic process purine nucleoside monophosphate metabolic process nucleoside monophosphate metabolic process nucleoside triphosphate biosynthetic process GTP metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036193	Adenylate kinase, active site lid domain superfamily	Homologous Superfamily
A, B	IPR028586	Adenylate kinase 3/4, mitochondrial	Family
A, B	IPR033690	Adenylate kinase, conserved site	Conserved Site
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR006259	Adenylate kinase subfamily	Family
A, B	IPR007862	Adenylate kinase, active site lid domain	Domain
A, B	IPR000850	Adenylate kinase/UMP-CMP kinase	Family
A, B	IPR028585	Adenylate kinase 4, mitochondrial	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P27144	osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor adrenal cortex carcinoma breast cancer interstitial cystitis lung cancer malignant pancreatic neoplasm non-small cell lung carcinoma osteoarthritis susceptibility 1 ovarian cancer Pick disease subependymal giant cell astrocytoma astrocytic tumor glioblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor adrenal cortex carcinoma breast cancer interstitial cystitis lung cancer malignant pancreatic neoplasm non-small cell lung carcinoma osteoarthritis susceptibility 1 ovarian cancer Pick disease subependymal giant cell astrocytoma astrocytic tumor glioblastoma invasive ductal breast carcinoma malignant ependymoma medulloblastoma oligodendroglioma Osteoarthrosis Deformans pancreatic ductal adenocarcinoma pilocytic astrocytoma tuberculosis atypical teratoid rhabdoid tumor hydrolethalus syndrome large cell medulloblastoma malignant mesothelioma nephrosclerosis osteoarthritis

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.