5N88

Crystal structure of antibody bound to viral protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
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)
A [auth H]	d5n88h_	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 [auth A]	d5n88a_	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)
D [auth E]	d5n88e1	All alpha proteins	N-cbl like	HIV integrase-binding domain	HIV integrase-binding domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d5n88e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth D]	d5n88d_	All alpha proteins	N-cbl like	HIV integrase-binding domain	HIV integrase-binding domain	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)
D [auth E]	SCOP2B Superfamily	HIV integrase-binding domain	8035439	3001321	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	HIV integrase-binding domain	8035439	3001321	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 [auth H]	PF07686	e5n88H1	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 [auth A]	PF07686	e5n88A1	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)
D [auth E]	PF11467	e5n88E1	A: alpha bundles	X: N-cbl like	H: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 (From Topology)	T: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70	F: PF11467	ECOD (1.6)
B [auth D]	PF11467	e5n88D1	A: alpha bundles	X: N-cbl like	H: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 (From Topology)	T: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70	F: PF11467	ECOD (1.6)

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
A [auth H], C [auth A]	VH59 antibody	VH	Homo sapiens (human)	IGHV3-4801, IGHV3-4804, IGHJ401, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	VH	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], C [auth A]	Heavy Chain	IGHV3	-	pc4 and sfrs1-interacting protein	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth E]	PF11467	Lens epithelium-derived growth factor (LEDGF) (LEDGF)	Lens epithelium-derived growth factor (LEDGF)	LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alph ...	LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure [1].	Domain
B [auth D]	PF11467	Lens epithelium-derived growth factor (LEDGF) (LEDGF)	Lens epithelium-derived growth factor (LEDGF)	LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alph ...	LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth A]	VH59 antibody	-	-	-
D [auth E]	PC4 and SFRS1-interacting protein	DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding supercoiled DNA binding transcription factor binding protein binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding supercoiled DNA binding transcription factor binding protein binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis spliceosomal complex assembly organic substance metabolic process protein-RNA complex organization cellular component assembly organic substance biosynthetic process protein-containing complex assembly ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis spliceosomal complex assembly organic substance metabolic process protein-RNA complex organization cellular component assembly organic substance biosynthetic process protein-containing complex assembly RNA processing cellular component organization or biogenesis mRNA splice site recognition RNA splicing protein-containing complex organization cellular metabolic process primary metabolic process mRNA 5'-splice site recognition gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process response to oxidative stress response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic 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 regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein-DNA complex organization chromatin organization chromatin remodeling	protein-containing complex intracellular anatomical structure protein-DNA complex chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen euchromatin nucleoplasm
B [auth D]	PC4 and SFRS1-interacting protein	DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding supercoiled DNA binding transcription factor binding protein binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding supercoiled DNA binding transcription factor binding protein binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis spliceosomal complex assembly organic substance metabolic process protein-RNA complex organization cellular component assembly organic substance biosynthetic process protein-containing complex assembly ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis spliceosomal complex assembly organic substance metabolic process protein-RNA complex organization cellular component assembly organic substance biosynthetic process protein-containing complex assembly RNA processing cellular component organization or biogenesis mRNA splice site recognition RNA splicing protein-containing complex organization cellular metabolic process primary metabolic process mRNA 5'-splice site recognition gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process response to oxidative stress response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic 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 regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein-DNA complex organization chromatin organization chromatin remodeling	protein-containing complex intracellular anatomical structure protein-DNA complex chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex chromatin chromosome cellular anatomical entity heterochromatin intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen euchromatin nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E]	IPR021567	Lens epithelium-derived growth factor, integrase-binding domain	Domain
D [auth E]	IPR036218	HIV integrase-binding domain superfamily	Homologous Superfamily
D [auth E]	IPR000313	PWWP domain	Domain
D [auth E]	IPR035441	TFIIS/LEDGF domain superfamily	Homologous Superfamily
B [auth D]	IPR021567	Lens epithelium-derived growth factor, integrase-binding domain	Domain
B [auth D]	IPR036218	HIV integrase-binding domain superfamily	Homologous Superfamily
B [auth D]	IPR000313	PWWP domain	Domain
B [auth D]	IPR035441	TFIIS/LEDGF domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth E]	Pharos: O75475	acute myeloid leukemia psoriasis astrocytic tumor Down syndrome invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer Sjogren syndrome Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma acute myeloid leukemia psoriasis astrocytic tumor Down syndrome invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer Sjogren syndrome Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma progressive supranuclear palsy tuberculosis dermatomyositis hepatocellular carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma
B [auth D]	Pharos: O75475	acute myeloid leukemia psoriasis astrocytic tumor Down syndrome invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer Sjogren syndrome Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma acute myeloid leukemia psoriasis astrocytic tumor Down syndrome invasive ductal breast carcinoma lung cancer malignant glioma ovarian cancer Sjogren syndrome Acute Myeloid Leukemia (AML-M2) atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant mesothelioma progressive supranuclear palsy tuberculosis dermatomyositis hepatocellular carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.