4KFZ

Crystal structure of LMO2 and anti-LMO2 VH complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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)
D	d4kfzd_	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)
C	d4kfzc_	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e4kfzA4	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00412	e4kfzA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: PF00412	ECOD (1.6)
B	F_UNCLASSIFIED	e4kfzB4	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00412	e4kfzB2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: PF00412	ECOD (1.6)
D	PF07686	e4kfzD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C	PF07686	e4kfzC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)
B	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV3	-	lmo-2	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00412	LIM domain (LIM)	LIM domain	This family represents two copies of the LIM structural domain.	Domain
C, D	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	LMO-2	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding transcription coregulator binding protein binding binding cation binding ion binding metal ion binding small molecule binding bHLH transcription factor binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding transcription coregulator binding protein binding binding cation binding ion binding metal ion binding small molecule binding bHLH transcription factor binding DNA-binding transcription factor binding identical protein binding RNA polymerase II-specific DNA-binding transcription factor binding	regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression 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 positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic 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 positive regulation of RNA biosynthetic process cellular process positive regulation of cellular biosynthetic process	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
C, D	Anti-LMO2 VH	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process	extracellular region extracellular space cellular anatomical entity blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular region extracellular space cellular anatomical entity blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001781	Zinc finger, LIM-type	Domain
C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D	IPR013106	Immunoglobulin V-set domain	Domain
C, D	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P25791	T-cell leukemia Precursor T-Cell Lymphoblastic Leukemia-Lymphoma subependymal giant cell astrocytoma tuberculosis acute T cell leukemia breast cancer glioblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis T-B+ severe combined immunodeficiency due to gamma chain deficiency ulcerative colitis adult T-cell leukemia/lymphoma breast carcinoma T-cell leukemia Precursor T-Cell Lymphoblastic Leukemia-Lymphoma subependymal giant cell astrocytoma tuberculosis acute T cell leukemia breast cancer glioblastoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis T-B+ severe combined immunodeficiency due to gamma chain deficiency ulcerative colitis adult T-cell leukemia/lymphoma breast carcinoma hematologic disease lung adenocarcinoma nasopharyngeal carcinoma ovarian cancer pilocytic astrocytoma Sjogren syndrome B-cell chronic lymphocytic leukemia cancer invasive ductal breast carcinoma lymphoplasmacytic lymphoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma
C, D	Pharos: P01764	B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm periodontitis ulcerative colitis cystic fibrosis lung adenocarcinoma non-small cell lung carcinoma plasma cell myeloma interstitial cystitis lung cancer osteosarcoma sinusitis

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.