2VYR | pdb_00002vyr

Structure of human MDM4 N-terminal domain bound to a single domain antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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)
L	d2vyrl_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d2vyrk_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d2vyrj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d2vyri_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2vyrh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d2vyrg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2vyrf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2vyre_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2vyra_	All alpha proteins	SWIB/MDM2 domain	SWIB/MDM2 domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2vyrb_	All alpha proteins	SWIB/MDM2 domain	SWIB/MDM2 domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2vyrd_	All alpha proteins	SWIB/MDM2 domain	SWIB/MDM2 domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2vyrc_	All alpha proteins	SWIB/MDM2 domain	SWIB/MDM2 domain	automated matches	automated matches	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)
A	SCOP2 Family	SWIB/MDM2 domain-like	8082224	4000971	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SWIB/MDM2 domain-like	8082225	3000287	SCOP2B (2022-06-29)
D	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	zf-CCCH_4	e2vyrL1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
K	zf-CCCH_4	e2vyrK1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
J	zf-CCCH_4	e2vyrJ1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
I	zf-CCCH_4	e2vyrI1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
H	zf-CCCH_4	e2vyrH1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
G	zf-CCCH_4	e2vyrG1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
F	zf-CCCH_4	e2vyrF1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
E	Response_reg	e2vyrE1	A: alpha bundles	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Response_reg	ECOD (develop294)
A	Peptidase_C2	e2vyrA1	A: alpha bundles	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Peptidase_C2	ECOD (develop294)
B	zf-CCCH_4	e2vyrB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
D	zf-CCCH_4	e2vyrD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)
C	zf-CCCH_4	e2vyrC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	1.10.245.10	Mainly Alpha	Orthogonal Bundle	MDM2	SWIB/MDM2 domain	CATH (4.3.0)
B	1.10.245.10	Mainly Alpha	Orthogonal Bundle	MDM2	SWIB/MDM2 domain	CATH (4.3.0)
D	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)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
E, F, G, H, I E, F, G, H, I, J, K, L	Single VH domain	VH	Homo sapiens (human)	IGHV3-2301, IGHV3-2303, IGHV3-23D01, IGHJ401, IGHJ402, IGHJ403	V-DOMAIN VH	IG	(VH)	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E, F, G, H, I E, F, G, H, I, J, K, L	Heavy Chain	IGHV3	-	mdm4 protein	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H, I E, F, G, H, I, J, K, L	HUMAN SINGLE DOMAIN ANTIBODY	-	-	-
A, B, C, D	MDM4 PROTEIN	enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity 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 enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity 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 RNA metabolic process regulation of primary 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary 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 negative regulation of cellular process 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular 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 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 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 negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator signal transduction negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus signal transduction by p53 class mediator negative regulation of signal transduction regulation of response to stimulus regulation of cell communication DNA damage response, signal transduction by p53 class mediator DNA damage response signal transduction in response to DNA damage catabolic process macromolecule catabolic process negative regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of catabolic process regulation of protein metabolic process protein catabolic process regulation of 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 intracellular organelle lumen intracellular organelle cellular anatomical structure 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 intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051652	MDM2/MDM4 and MUL1	Family
A, B, C, D	IPR003121	SWIB/MDM2 domain	Domain
A, B, C, D	IPR016495	p53 negative regulator Mdm2/Mdm4	Family
A, B, C, D	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A, B, C, D	IPR036885	SWIB/MDM2 domain superfamily	Homologous Superfamily
A, B, C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR001876	Zinc finger, RanBP2-type	Domain
A, B, C, D	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D	IPR015458	MDM4	Family

Pharos: Disease Associations Pharos Homepage Annotation

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

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.