Structural definition of a conserved neutralization epitope on HIV-1 gp120.

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HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12

Annotation data related to this entry.

2NY7

FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)

FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly 1 (gz) (A+S)
Biological Assembly 2 (gz) (S)
Biological Assembly 3 (gz) (S)
Biological Assembly 4 (gz) (S)
Biological Assembly 5 (gz) (S)

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Domain Annotation: SCOP Classification (version 1.75)

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Domain Info	Class	Fold	Superfamily	Family	Domain	Species
d2ny7h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	Human (Homo sapiens), cluster 1 [TaxId: 9606]
d2ny7h2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain- like)	Immunoglobulin heavy chain gamma constant domain 1, CH1- gamma	Human (Homo sapiens) [TaxId: 9606]
d2ny7l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL- kappa	Human (Homo sapiens), cluster 3.1 [TaxId: 9606]
d2ny7l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain- like)	Immunoglobulin light chain kappa constant domain, CL- kappa	Human (Homo sapiens) [TaxId: 9606]
d2ny7g1	Alpha and beta proteins (a+b)	gp120 core	gp120 core	gp120 core	gp120 core	Human immunodeficiency virus type 1 [TaxId: 11676]

Domain Annotation: CATH Classification (version 3.5.0)

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Domain	Class	Architecture	Topology	Homology
2ny7G00	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120; Chain G	HIV Envelope Protein Gp120; Chain G
2ny7H01	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins
2ny7H02	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins
2ny7L01	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins
2ny7L02	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins

Protein Family Annotation: Pfam Classification

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Chain	Pfam Accession	Pfam Family Identifier	Pfam Description	Type	Comment
H	PF13927	Ig_3	Immunoglobulin domain	Domain	This family contains immunoglobulin-like domains. Source: Pfam
L	PF08205	C2-set_2	CD80-like C2-set immunoglobulin domain	Domain	These domains belong to the immunoglobulin superfamily. Source: Pfam
G	PF00516	GP120	Envelope glycoprotein GP120	Family
H	PF07654	C1-set	Immunoglobulin C1-set domain	Domain	Source: Pfam
G	PF00516	GP120	Envelope glycoprotein GP120	Family
G	PF00516	GP120	Envelope glycoprotein GP120	Family
H	PF07686	V-set	Immunoglobulin V-set domain	Domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. Source: Pfam
L	PF00047	ig	Immunoglobulin domain	Domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain. Source: Pfam
L	PF13927	Ig_3	Immunoglobulin domain	Domain	This family contains immunoglobulin-like domains. Source: Pfam
L	PF07686	V-set	Immunoglobulin V-set domain	Domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. Source: Pfam
L	PF07654	C1-set	Immunoglobulin C1-set domain	Domain	Source: Pfam
L	PF13927	Ig_3	Immunoglobulin domain	Domain	This family contains immunoglobulin-like domains. Source: Pfam

Gene Product Annotation: GO Terms

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Polymer	Molecular Function	Biological Process	Cellular Component
ENVELOPE GLYCOPROTEIN GP120 (2NY7:G)	none	none	viral envelope
ANTIBODY b12, HEAVY CHAIN (2NY7:H)	none	none	none
ANTIBODY b12, LIGHT CHAIN (2NY7:L)	antigen binding	retina homeostasis receptor-mediated endocytosis immune response complement activation complement activation, classical pathway Fc-epsilon receptor signaling pathway Fc-gamma receptor signaling pathway involved in phagocytosis innate immune response regulation of immune response	extracellular region extracellular space plasma membrane extracellular vesicular exosome blood microparticle

Annotations in orange boxes have been gathered from external resources.

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