SUPERFAMILY 1.75 HMM library and genome assignments server

gp120 core superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   gp120 core [ 56501]
Superfamily:   gp120 core [ 56502]
Families:   gp120 core [ 56503]


Superfamily statistics
Genomes (0) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 0 212,328 14
Proteins 0 174,943 14


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)binding00.00002116Least InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) binding 0.00002116 Least Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Biological processClathrin-mediated endocytosis of virus by host0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Cellular componentViral envelope protein0Highly InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000777 SSF56502 Protein matches
Abstract

The entry of HIV requires interaction of viral GP120, an envelope glycoprotein with human T-cell surface glycoprotein CD4 and a chemokine receptor on the cell surface. These envelope glycoproteins are found in HIV types 1 and 2, and Simian Immunodeficiency virus (SIV).


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 3 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a gp120 core domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 3 hidden Markov models representing the gp120 core superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]