You can use BioMart web interface in Ensembl. There's a specific filter for genes with a given domain and you can use a broad range of cross ref identifiers (Pfam, Interpro, etc.). I really like this approach 'cause it permits to relate domain with gene structure, to get sequence variation and a lot of other very useful things. Of course, you can't obtain all kinds of raw data (sequences, structures, etc.).
Already nice solutions here: if it is for one or two protein domain families you can get the list of all domains in an organism using the Species tab(Species distribution) in Pfam. Click on the Check-box next to your organism of interest; then click on Download to download tezt file with sequence accessions or sequences in FASTA format. Pfam also provides a list of domain architecture with FVYE in human. Here is the link to access architecture of 74 Sequences with FYVE domain.
Another way to get them is using the advanced search in Uniprot. First select the "Domain" option in the field box and type "FYVE". Then click "Add & Search" and select "Organism" in the field box and type/select "Homo sapiens".