5VK1

Crystal structure of human MDM4 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	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)
A	PF02201	e5vk1A1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
G	PF02201	e5vk1G1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
I	PF02201	e5vk1I1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
M	PF02201	e5vk1M1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
C	PF02201	e5vk1C1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
E	PF02201	e5vk1E1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
K	PF02201	e5vk1K1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)
O	PF02201	e5vk1O1	A: alpha arrays	X: SWIB/MDM2 domain (From Topology)	H: SWIB/MDM2 domain (From Topology)	T: SWIB/MDM2 domain	F: PF02201	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

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, M, O	Protein Mdm4	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding protein binding enzyme binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis regulation of protein stability regulation of biological quality protein stabilization developmental process heart development multicellular organismal process animal organ development ventricular septum development circulatory system development multicellular organism development cardiac septum development cardiac chamber development anatomical structure development cardiac ventricle development system development negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death 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 organonitrogen compound metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal mesenchyme morphogenesis endocardial cushion morphogenesis heart morphogenesis mesenchyme development tissue development tissue morphogenesis anatomical structure morphogenesis endocardial cushion development animal organ morphogenesis heart valve development cardiac atrium development atrial septum development negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation signaling signal transduction by p53 class mediator DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication DNA damage response signal transduction in response to DNA damage signal transduction catabolic process macromolecule catabolic process negative regulation of protein catabolic process negative regulation of protein metabolic process organonitrogen compound catabolic process negative regulation of catabolic process regulation of protein metabolic process protein catabolic process regulation of catabolic process organic substance catabolic process regulation of protein catabolic process cell cycle regulation of cell cycle transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II atrioventricular valve development heart valve morphogenesis atrioventricular valve morphogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex transcription regulator complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex transcription regulator complex transcription repressor complex
B, D, F, H, J B, D, F, H, J, L, N, P	Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR003121	SWIB/MDM2 domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR016495	p53 negative regulator Mdm2/Mdm4	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036885	SWIB/MDM2 domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001876	Zinc finger, RanBP2-type	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001841	Zinc finger, RING-type	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR015458	MDM4	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: O15151	breast carcinoma glioblastoma giant cell glioblastoma pneumoconiosis bagassosis medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor androgenetic alopecia retinoblastoma bladder benign neoplasm Unipolar Depression breast cancer urinary bladder neoplasm breast carcinoma glioblastoma giant cell glioblastoma pneumoconiosis bagassosis medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor androgenetic alopecia retinoblastoma bladder benign neoplasm Unipolar Depression breast cancer urinary bladder neoplasm estrogen-receptor negative breast cancer juvenile dermatomyositis malignant ependymoma myopathy osteosarcoma Pick disease prostate carcinoma attention deficit hyperactivity disorder, inattentive type sarcoma bladder carcinoma in situ urinary bladder cancer large cell medulloblastoma malignant mesothelioma ovarian cancer psoriasis tuberculosis brain glioma urinary bladder carcinoma diabetes mellitus major depressive disorder

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, L, N, P	9E7	Parent Component: LYS
B, D, F, H, J B, D, F, H, J, L, N, P	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B, D, F, H, J B, D, F, H, J, L, N, P	NH2	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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 R01GM133198.