7Z1Z | pdb_00007z1z

MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth Q]	SCOP2B Superfamily	HIV integrase-binding domain	8035439	3001321	SCOP2B (2022-06-29)
I [auth R]	SCOP2B Superfamily	HIV integrase-binding domain	8035439	3001321	SCOP2B (2022-06-29)
U [auth P]	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
S [auth N]	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
R [auth M]	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
Q [auth L]	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
P [auth K]	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
N [auth I]	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	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)
J [auth Q]		e7z1zQ1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
I [auth R]		e7z1zR1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
U [auth P]		e7z1zP1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
T [auth O]		e7z1zO1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
S [auth N]		e7z1zN1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
R [auth M]	V-set	e7z1zM1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
Q [auth L]	V-set	e7z1zL1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
P [auth K]	V-set	e7z1zK1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
O [auth J]		e7z1zJ1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
N [auth I]	V-set	e7z1zI1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
H		e7z1zH1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
G		e7z1zG1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
F		e7z1zF1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
E	V-set	e7z1zE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
D	V-set	e7z1zD1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
C	V-set	e7z1zC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)
B		e7z1zB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F:	ECOD (v294.1)
A	V-set	e7z1zA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth Q]	1.20.930.10	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (utative)
I [auth R]	1.20.930.10	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (utative)
T [auth O]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
S [auth N]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
S [auth N]	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
R [auth M]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
Q [auth L]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
P [auth K]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
O [auth J]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
N [auth I]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
G	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
F	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth R], J [auth Q]	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
M [auth U], X [auth a]	DNA (5'-D(PTPTPGPAPTPTPAPGPGPGPTPG)-3')	-	-	-
L [auth W], W [auth Z]	DNA (37-MER)	-	-	-
K [auth X], V [auth Y]	DNA (5'-D(GPCPTPGPCPGPAPGPAPTPCPCPGPCPTPCPCPGPGPTP*G)-3')	-	-	-
I [auth R], J [auth Q]	PC4 and SFRS1-interacting protein	DNA binding double-stranded DNA binding 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 RNA binding	ribonucleoprotein complex biogenesis 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 ribonucleoprotein complex biogenesis 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 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 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 biological regulation regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II 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 chromatin organization chromatin remodeling	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen euchromatin nucleoplasm
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	Pol polyprotein	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity hydrolase activity, acting on acid anhydrides cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleoside phosphate metabolic process nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process DNA integration proteolysis protein metabolic process	viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth R], J [auth Q]	IPR021567	Lens epithelium-derived growth factor, integrase-binding domain	Domain
I [auth R], J [auth Q]	IPR036218	HIV integrase-binding domain superfamily	Homologous Superfamily
I [auth R], J [auth Q]	IPR000313	PWWP domain	Domain
I [auth R], J [auth Q]	IPR035441	TFIIS/LEDGF domain superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR029054	dUTPase-like	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR018061	Retropepsins	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR033704	dUTPase, trimeric	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H, N [auth I], O [auth J], P [auth K], Q [auth L], R [auth M], S [auth N], T [auth O], U [auth P]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth R], J [auth Q]	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