3ZKF | pdb_00003zkf

Structure of LC8 in complex with Nek9 phosphopeptide

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DLC-like	8034979	3000821	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DLC-like	8034979	3000821	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DLC-like	8034979	3000821	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DLC-like	8034979	3000821	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	DLC-like	8034979	3000821	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	DLC-like	8034979	3000821	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	Dynein_light	e3zkfA1	A: a+b two layers	X: DLC (From Topology)	H: DLC (From Topology)	T: DLC	F: Dynein_light	ECOD (1.6)
C	Dynein_light	e3zkfC1	A: a+b two layers	X: DLC (From Topology)	H: DLC (From Topology)	T: DLC	F: Dynein_light	ECOD (1.6)
E	Dynein_light	e3zkfE1	A: a+b two layers	X: DLC (From Topology)	H: DLC (From Topology)	T: DLC	F: Dynein_light	ECOD (1.6)
G	Dynein_light	e3zkfG1	A: a+b two layers	X: DLC (From Topology)	H: DLC (From Topology)	T: DLC	F: Dynein_light	ECOD (1.6)
I	Dynein_light	e3zkfI1	A: a+b two layers	X: DLC (From Topology)	H: DLC (From Topology)	T: DLC	F: Dynein_light	ECOD (1.6)
K	Dynein_light	e3zkfK1	A: a+b two layers	X: DLC (From Topology)	H: DLC (From Topology)	T: DLC	F: Dynein_light	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.740.10	Alpha Beta	2-Layer Sandwich	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	CATH (4.3.0)
C	3.30.740.10	Alpha Beta	2-Layer Sandwich	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	CATH (4.3.0)
E	3.30.740.10	Alpha Beta	2-Layer Sandwich	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	CATH (4.3.0)
G	3.30.740.10	Alpha Beta	2-Layer Sandwich	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	CATH (4.3.0)
I	3.30.740.10	Alpha Beta	2-Layer Sandwich	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	CATH (4.3.0)
K	3.30.740.10	Alpha Beta	2-Layer Sandwich	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	Protein Inhibitor Of Neuronal Nitric Oxide Synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF01221	Dynein light chain type 1 (Dynein_light)	Dynein light chain type 1		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	DYNEIN LIGHT CHAIN 1, CYTOPLASMIC	enzyme regulator activity catalytic activity, acting on a nucleic acid hydrolase activity enzyme inhibitor activity DNA nuclease activity deoxyribonuclease inhibitor activity molecular function inhibitor activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds molecular function regulator activity nuclease inhibitor activity catalytic activity protein binding enzyme regulator activity catalytic activity, acting on a nucleic acid hydrolase activity enzyme inhibitor activity DNA nuclease activity deoxyribonuclease inhibitor activity molecular function inhibitor activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds molecular function regulator activity nuclease inhibitor activity catalytic activity protein binding binding dynein intermediate chain binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process organelle assembly plasma membrane bounded cell projection organization motile cilium assembly cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process organelle assembly plasma membrane bounded cell projection organization motile cilium assembly cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization cell projection assembly apoptotic process cell death programmed cell death regulation of cellular process DNA-templated DNA replication maintenance of fidelity negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of DNA-templated DNA replication regulation of DNA strand resection involved in replication fork processing DNA strand resection involved in replication fork processing negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA strand resection involved in replication fork processing regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process DNA-templated DNA replication regulation of biological process negative regulation of DNA replication negative regulation of metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication regulation of DNA-templated DNA replication metabolic process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process replication fork processing regulation of DNA metabolic process regulation of DNA replication cellular localization transport intracellular transport intraciliary retrograde transport establishment of localization protein-containing complex localization localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process intraciliary transport phosphorylation negative regulation of phosphate metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of phosphorus metabolic process regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation phosphorus metabolic process developmental process multicellular organismal process head development animal organ development brain development nervous system development substantia nigra development multicellular organism development central nervous system development midbrain development anatomical structure development neural nucleus development system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell projection cilium plasma membrane bounded cell projection tertiary granule membrane membrane intracellular vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell projection cilium plasma membrane bounded cell projection tertiary granule membrane membrane intracellular vesicle endomembrane system tertiary granule cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle secretory granule secretory vesicle vesicle organelle membrane secretory granule membrane centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol ciliary tip cell periphery plasma membrane mitotic spindle spindle chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome ficolin-1-rich granule membrane ficolin-1-rich granule site of double-strand break site of DNA damage protein-containing complex cytoplasmic dynein complex catalytic complex dynein complex microtubule associated complex polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer nucleus
B, D, F, H, J B, D, F, H, J, L	NEK9 PROTEIN	protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity histone H3S57 kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H3 kinase activity histone modifying activity catalytic activity histone kinase activity histone H2AS121 kinase activity histone H2A kinase activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity histone H3S57 kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H3 kinase activity histone modifying activity catalytic activity histone kinase activity histone H2AS121 kinase activity histone H2A kinase activity Rho-dependent protein serine/threonine kinase activity AMP-activated protein kinase activity histone H2AT120 kinase activity enzyme regulator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity molecular function regulator activity protein kinase activator activity kinase regulator activity DNA-dependent protein kinase activity histone H3T45 kinase activity histone H2AXS139 kinase activity histone H2AX kinase activity histone H4S1 kinase activity histone H4 kinase activity eukaryotic translation initiation factor 2alpha kinase activity protein serine kinase activity 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 binding kinase binding enzyme binding protein kinase binding histone H3T11 kinase activity histone H3S28 kinase activity histone H3T6 kinase activity 3-phosphoinositide-dependent protein kinase activity histone H2B kinase activity histone H2BS36 kinase activity histone H3T3 kinase activity histone H2AS1 kinase activity ribosomal protein S6 kinase activity histone H3S10 kinase activity cation binding metal ion binding histone H2BS14 kinase activity	cellular process cell cycle mitotic cell cycle regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation regulation of cell cycle cell division	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR037177	Dynein light chain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR019763	Dynein light chain, type 1/2, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K	IPR001372	Dynein light chain, type 1/2	Family
B, D, F, H, J B, D, F, H, J, L	IPR000408	Regulator of chromosome condensation, RCC1	Repeat
B, D, F, H, J B, D, F, H, J, L	IPR000719	Protein kinase domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR009091	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR042767	Serine/threonine-protein kinase Nek9, catalytic domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR051997	Serine/threonine-protein kinase NEK	Family
B, D, F, H, J B, D, F, H, J, L	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K	Pharos: P63167	brain ischemia acute myeloid leukemia breast cancer Emery-Dreifuss muscular dystrophy lung cancer ovarian cancer Becker muscular dystrophy Cerebral Ischemia hepatocellular carcinoma lymphoplasmacytic lymphoma plasma cell myeloma Duchenne muscular dystrophy juvenile dermatomyositis myopathy tuberculosis
B, D, F, H, J B, D, F, H, J, L	Pharos: Q8TD19	arthrogryposis, Perthes disease, and upward gaze palsy nevus comedonicus syndrome NEK9-related lethal skeletal dysplasia arthrogryposis breast cancer heart disease malignant mesothelioma osteosarcoma dermatomyositis large cell medulloblastoma ovarian cancer astrocytic tumor Gaucher disease lung cancer thrombocytopenia due to immune destruction

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, L	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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.