Annotations: 3LNJ

Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha)

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)
E	SCOP2B Superfamily	SWIB/MDM2 domain-like	8037458	3000287	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SWIB/MDM2 domain-like	8037458	3000287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SWIB/MDM2 domain-like	8037458	3000287	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)
E	Tachylectin	e3lnjE1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Tachylectin	ECOD (v295.2)
C	Tachylectin	e3lnjC1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Tachylectin	ECOD (v295.2)
A	Tachylectin	e3lnjA1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Tachylectin	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	1.10.245.10	Mainly Alpha	Orthogonal Bundle	MDM2	SWIB/MDM2 domain	CATH (4.3.0)
C	1.10.245.10	Mainly Alpha	Orthogonal Bundle	MDM2	SWIB/MDM2 domain	CATH (4.3.0)
A	1.10.245.10	Mainly Alpha	Orthogonal Bundle	MDM2	SWIB/MDM2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF02201	SWIB/MDM2 domain (SWIB)	SWIB/MDM2 domain	This family includes the SWIB domain and the MDM2 domain [1]. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. Thi ...	This family includes the SWIB domain and the MDM2 domain [1]. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	D-peptide inhibitor	-	-	-
A, C, E	E3 ubiquitin-protein ligase Mdm2	protein binding binding signaling receptor binding peroxisome proliferator activated receptor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity SUMO transferase activity protein binding binding signaling receptor binding peroxisome proliferator activated receptor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity SUMO transferase activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding ligase activity identical protein binding p53 binding protein domain specific binding RNA binding rRNA binding 5S rRNA binding nucleic acid binding ubiquitin binding ubiquitin-like protein binding ribonucleoprotein complex binding protein-containing complex binding receptor serine/threonine kinase binding NEDD8 transferase activity NEDD8 ligase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding disordered domain specific binding	response to stimulus response to chemical response to xenobiotic stimulus response to oxygen-containing compound response to formaldehyde protein destabilization regulation of protein stability biological regulation regulation of biological quality regulation of biological process regulation of cellular process catabolic process regulation of protein metabolic process primary metabolic process response to stimulus response to chemical response to xenobiotic stimulus response to oxygen-containing compound response to formaldehyde protein destabilization regulation of protein stability biological regulation regulation of biological quality regulation of biological process regulation of cellular process catabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process macromolecule catabolic process regulation of primary metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone cellular response to hormone stimulus regulation of biosynthetic process positive regulation of biological process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway regulation of signal transduction by p53 class mediator negative regulation of cellular process signal transduction intrinsic apoptotic signaling pathway negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process signal transduction by p53 class mediator cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway response to antibiotic protein autoubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal peptidyl-lysine modification protein sumoylation cellular response to alkaloid response to alkaloid positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process proteasomal protein catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process response to nutrient levels response to vitamin B1 response to alcohol response to nutrient response to vitamin cellular response to vitamin B1 cellular response to nutrient levels cellular response to alcohol cellular response to vitamin cellular response to nutrient fibroblast activation multicellular organismal process cell activation response to toxic substance regulation of neuron projection development regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development 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 nervous system development negative regulation of neuron projection development generation of neurons neuron development animal gross anatomical part developmental process regulation of plasma membrane bounded cell projection organization response to metal ion response to iron ion protein polyubiquitination cellular response to antibiotic response to lipid response to steroid hormone response to immobilization stress response to water-immersion restraint stress response to estrogen cellular response to estrogen stimulus RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process import into cell regulation of localization cellular localization receptor internalization transport postsynaptic neurotransmitter receptor internalization regulation of receptor internalization vesicle-mediated transport vesicle-mediated transport in synapse localization establishment of localization in cell regulation of postsynaptic neurotransmitter receptor internalization regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis endocytosis receptor-mediated endocytosis response to ether cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly establishment of protein localization regulation of developmental process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation cellular response to abiotic stimulus response to gamma radiation supramolecular fiber organization amyloid fibril formation regulation of cellular response to stress DNA damage response, signal transduction by p53 class mediator regulation of response to stress negative regulation of DNA damage response, signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator DNA damage response signal transduction in response to DNA damage regulation of vascular associated smooth muscle cell proliferation cell population proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation regulation of vascular associated smooth muscle cell migration positive regulation of locomotion vascular associated smooth muscle cell migration regulation of cell motility regulation of smooth muscle cell migration positive regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of vascular associated smooth muscle cell migration cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species regulation of protein localization nucleocytoplasmic transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport intracellular protein localization nuclear export regulation of protein export from nucleus regulation of intracellular transport regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport regulation of protein transport protein export from nucleus positive regulation of protein export from nucleus positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport modulation of chemical synaptic transmission regulation of protein catabolic process at postsynapse, modulating synaptic transmission synaptic signaling postsynaptic modulation of chemical synaptic transmission trans-synaptic signaling cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling response to light stimulus response to UV cellular response to UV-C response to UV-C cellular response to light stimulus cellular response to UV cellular response to growth factor stimulus response to growth factor regulation of protein maturation negative regulation of proteolysis negative regulation of protein maturation protein maturation regulation of proteolysis proteolysis negative regulation of protein metabolic process negative regulation of gene expression regulation of protein processing protein processing negative regulation of protein processing cell cycle regulation of cell cycle positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle response to cocaine protein localization to organelle protein localization to nucleus response to magnesium ion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane vesicle organelle membrane endocytic vesicle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen cell periphery plasma membrane nucleoplasm protein-containing complex postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR003121	SWIB/MDM2 domain	Domain
A, C, E	IPR016495	p53 negative regulator Mdm2/Mdm4	Family
A, C, E	IPR036885	SWIB/MDM2 domain superfamily	Homologous Superfamily
A, C, E	IPR044080	MDM2, modified RING finger, HC subclass	Domain
A, C, E	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C, E	IPR001876	Zinc finger, RanBP2-type	Domain
A, C, E	IPR001841	Zinc finger, RING-type	Domain
A, C, E	IPR028340	E3 ubiquitin-protein ligase Mdm2	Family
A, C, E	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E	: Q00987	melanoma cancer Li-Fraumeni syndrome prostate cancer HIV infectious disease non-small cell lung carcinoma breast carcinoma well-differentiated liposarcoma male infertility precancerous condition gastric carcinoma hematologic disease SAPHO syndrome Subfertility, Male lipoma melanoma cancer Li-Fraumeni syndrome prostate cancer HIV infectious disease non-small cell lung carcinoma breast carcinoma well-differentiated liposarcoma male infertility precancerous condition gastric carcinoma hematologic disease SAPHO syndrome Subfertility, Male lipoma acute lymphoblastic leukemia lymphatic system disease amyotrophic lateral sclerosis breast cancer cutaneous melanoma peripheral nervous system disease exocrine pancreatic carcinoma glioblastoma hepatocellular carcinoma sarcoma juvenile dermatomyositis urinary bladder cancer lung cancer acute myeloid leukemia malignant colon neoplasm atypical lipomatous tumor malignant pancreatic neoplasm myopathy connective tissue disease osteosarcoma Dedifferentiated liposarcoma peripheral neuropathy gastric cancer primitive neuroectodermal tumor glioma psoriasis subependymal giant cell astrocytoma lung disease acute promyelocytic leukemia malignant mesothelioma atypical teratoid rhabdoid tumor breast disease colorectal adenocarcinoma Crohn disease ovarian cancer Emery-Dreifuss muscular dystrophy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F	DAL	: AA0111 , AA0191 : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
B, D, F	DAR	: AA0111 , AA0191
B, D, F	DGL	: AA0111 , AA0191
B, D, F	DLE	: AA0111 , AA0191 , AA0197 : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-leucine MOD:00204
B, D, F	DLY	: AA0111 , AA0191 , AA0197
B, D, F	DSG	: AA0111 , AA0191 , AA0197 , AA0196 , AA0622 : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-leucine MOD:00204 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985
B, D, F	DTH	: AA0111 , AA0191 , AA0197 , AA0196 , AA0622 , AA0199 : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-leucine MOD:00204 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-allo-threonine MOD:00863
B, D, F	DTR	: AA0111 , AA0191 , AA0197 , AA0196 , AA0622 , AA0199 , AA0198 : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862 , D-leucine MOD:00204 , D-asparagine MOD:00203 , 2-(L-cystein-S-yl)-D-asparagine MOD:01985 , D-allo-threonine MOD:00863 , D-tryptophan MOD:00205
B, D, F	DTY	: AA0111 , AA0191 , AA0197 , AA0196 , AA0622 , AA0199 , AA0198