Structure of PDB 5k78 Chain D Binding Site BS04

Receptor Information

>5k78 Chain D (length=349) Species: 5759 (Entamoeba histolytica)

QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEAD
LVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNAESSNVLLHLYNGG
FVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSL
FHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKK
DGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKN
AISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLS
KRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 5k78 Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5k78 The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures
• Resolution: 2.64 Å
• Binding residue (original residue number in PDB): C14 H16 H232
• Binding residue (residue number reindexed from 1): C10 H12 H228
• Annotation score: 4

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:5k78, PDBe:5k78, PDBj:5k78
• PDBsum: 5k78
• UniProt: C4M1P9|DBR1_ENTH1 Lariat debranching enzyme (Gene Name=DBR1)