Structure of PDB 8y7e Chain 6

Receptor sequence

>8y7e6 (length=105) Species: 9606 (Homo sapiens)

AKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNY
GSYQGRCVICGGPGVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYE
RKKYG

3D structure

• PDB: 8y7e Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome
• Chain: 6
• Resolution: 4.66 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	6	H4 H5 Y36 F99 R102 K103	H3 H4 Y35 F98 R101 K102
BS02	rna	6	S94 D97 E101 R102	S93 D96 E100 R101
BS03	ZN	6	C23 C26 C58 C61	C22 C25 C57 C60
BS04	ZN	6	C11 C46 C49 C85	C10 C45 C48 C84
BS05	ZN	6	C30 C33 C72 C75	C29 C32 C71 C74

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing
• GO:0045893 positive regulation of DNA-templated transcription
• GO:0048863 stem cell differentiation
• GO:1903241 U2-type prespliceosome assembly

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005684 U2-type spliceosomal complex
• GO:0005686 U2 snRNP
• GO:0005689 U12-type spliceosomal complex
• GO:0016363 nuclear matrix
• GO:0016607 nuclear speck
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071011 precatalytic spliceosome

External links

• PDB: RCSB:8y7e, PDBe:8y7e, PDBj:8y7e
• PDBsum: 8y7e
• PubMed: 38484052
• UniProt: Q7RTV0|PHF5A_HUMAN PHD finger-like domain-containing protein 5A (Gene Name=PHF5A)