Structure of PDB 5k77 Chain D Binding Site BS01

Receptor Information

>5k77 Chain D (length=349) Species: 5759 (Entamoeba histolytica)

QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEAD
LVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNAESSNVLLHLYNGG
FVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSL
FHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKK
DGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKN
AISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLS
KRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI

Ligand information

>5k77 Chain Y (length=4)

aaca

....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k77 Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.
• Resolution: 2.17 Å
• Binding residue (original residue number in PDB): H16 Q47 V60 P61 Y64 I132 K134 F136 F155 H156 K249
• Binding residue (residue number reindexed from 1): H12 Q43 V56 P57 Y60 I128 K130 F132 F151 H152 K245

Enzymatic activity

• Enzyme Commision number: 3.1.4.-

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005506 iron ion binding
• GO:0008270 zinc ion binding
• GO:0008419 RNA lariat debranching enzyme activity
• GO:0016787 hydrolase activity
• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000375 RNA splicing, via transesterification reactions
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0048471 perinuclear region of cytoplasm

External links

• PDB: RCSB:5k77, PDBe:5k77, PDBj:5k77
• PDBsum: 5k77
• PubMed: 27930312
• UniProt: C4M1P9|DBR1_ENTH1 Lariat debranching enzyme (Gene Name=DBR1)