1Z9E

Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1z9ea1	All alpha proteins	N-cbl like	HIV integrase-binding domain	HIV integrase-binding domain	PC4 and SFRS1-interacting protein, PSIP1	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	HIV integrase-binding domain	8023059	4001336	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HIV integrase-binding domain	8035439	3001321	SCOP2 (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	LEDGF	e1z9eA1	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: LEDGF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.930.10	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	PC4 and SFRS1 interacting protein 2	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 chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor 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 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 RNA biosynthetic process cellular component organization cellular component biogenesis nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process RNA biosynthetic process cellular component organization cellular component biogenesis nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly 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 nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic 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 biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process chromatin organization chromatin remodeling	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity heterochromatin non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity heterochromatin 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
A	IPR021567	Lens epithelium-derived growth factor, integrase-binding domain	Domain
A	IPR036218	HIV integrase-binding domain superfamily	Homologous Superfamily
A	IPR000313	PWWP domain	Domain
A	IPR035441	TFIIS/LEDGF domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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 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.