Structure of PDB 6ieg Chain B Binding Site BS01

Receptor Information
>6ieg Chain B (length=911) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADLMPRVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDA
FQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIK
ALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEV
MREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQF
AEWICHLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDN
FNTAMQVLRDSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDF
NTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLP
ILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRW
ISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNS
AFHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQ
YNKIVIPNEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVK
VKNEGDDFGWGVVVNFSKKSDPLYVVEVLLRCSKESLKNSAAKPAKPDEK
GEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSIQEVQKRFPDG
IPLLDPIDDMGIQDQGLKKVIQKVEAFEHRMYSHPLHNDPNLETVYTLCE
KKAQIAIDIKSAKRELKTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRV
ACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTE
QLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATG
ATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEG
ITKIKRDIVFA
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6ieg Chain B Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ieg NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.
Resolution3.55 Å
Binding residue
(original residue number in PDB)		F138 D141 T163 A165 G166 K167 T168
Binding residue
(residue number reindexed from 1)		F46 D49 T71 A73 G74 K75 T76
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0000398 mRNA splicing, via spliceosome
GO:0000460 maturation of 5.8S rRNA
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0006401 RNA catabolic process
GO:0006974 DNA damage response
GO:0008380 RNA splicing
GO:0016076 snRNA catabolic process
Cellular Component
GO:0000176 nuclear exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005730 nucleolus
GO:0016607 nuclear speck
GO:0031499 TRAMP complex
GO:0071013 catalytic step 2 spliceosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ieg, PDBe:6ieg, PDBj:6ieg
PDBsum6ieg
PubMed30842217
UniProtP42285|MTREX_HUMAN Exosome RNA helicase MTR4 (Gene Name=MTREX)

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