6B72 | pdb_00006b72

A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Regulatory factor Nef	8086598	3000353	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Regulatory factor Nef	8086598	3000353	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Regulatory factor Nef	8086598	3000353	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Regulatory factor Nef	8086598	3000353	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	OB_NTP_bind	e6b72A1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)
B	OB_NTP_bind	e6b72B1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)
C	OB_NTP_bind	e6b72C1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)
D	OB_NTP_bind	e6b72D1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)
E	OB_NTP_bind	e6b72E1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)
F	OB_NTP_bind	e6b72F1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (utative)
B	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (utative)
C	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (utative)
D	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (utative)
E	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (utative)
F	3.30.62.10	Alpha Beta	2-Layer Sandwich	Nef Regulatory Factor	Nef Regulatory Factor	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00469	Negative factor, (F-Protein) or Nef (F-protein)	Negative factor, (F-Protein) or Nef	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Protein Nef	SH3 domain binding protein binding binding protein domain specific binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding SH3 domain binding protein binding binding protein domain specific binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I symbiont-mediated suppression of host antigen processing and presentation modulation of process of another organism symbiont-mediated suppression of host adaptive immune response symbiont entry into host cell viral process symbiont entry into host symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I symbiont-mediated suppression of host antigen processing and presentation modulation of process of another organism symbiont-mediated suppression of host adaptive immune response symbiont entry into host cell viral process symbiont entry into host viral life cycle endocytosis involved in viral entry into host cell symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II cellular response to stimulus regulation of cellular process positive regulation of phosphorylation response to stimulus regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process cell surface receptor protein tyrosine kinase signaling pathway regulation of primary metabolic process cell communication cellular component biogenesis positive regulation of metabolic process cellular component assembly phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process signal transduction phosphorus metabolic process protein modification process positive regulation of protein phosphorylation activation of transmembrane receptor protein tyrosine kinase activity regulation of biological process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation signaling positive regulation of protein metabolic process positive regulation of biological process cellular component organization positive regulation of molecular function positive regulation of protein modification process protein-containing complex assembly cellular component organization or biogenesis protein metabolic process positive regulation of protein kinase activity enzyme-linked receptor protein signaling pathway positive regulation of cellular process cell surface receptor signaling pathway protein-containing complex organization biological regulation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process cellular process regulation of phosphorylation symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host autophagy symbiont-mediated perturbation of host autophagy	cellular anatomical structure membrane extracellular region virion component host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm cellular anatomical structure membrane extracellular region virion component host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm host cell endomembrane system host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001558	HIV negative factor Nef	Family
A, B, C, D, E A, B, C, D, E, F	IPR027480	HIV-1 Nef protein, anchor domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR027481	HIV-1 Nef protein, core domain superfamily	Homologous Superfamily

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.