Structure of PDB 6ieh Chain B Binding Site BS01

Receptor Information
>6ieh Chain B (length=929) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQREA
IQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQ
KYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMREVA
WVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWIC
HLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNTAM
QVLRDAGDSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNT
DEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPIL
KETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWIS
SGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAF
HLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGVVEKVKNSEEQYN
KIVIPNEESVVIYYKIRQQLAKLGKEIEEYIHKPKYCLPFLQPGRLVKVK
NEGDDFGWGVVVNFSKKSNVKPNSGELDPLYVVEVLLRCSKESLKNSATE
AAKPAKPDEKGEMQVVPVLVHLLSAISSVRLYIPKDLRPVDNRQSVLKSI
QEVQKRFPDGIPLLDPIDDMGIQDQGLKKVIQKVEAFEHRMYSHPLHNDP
NLETVYTLCEKKAQIAIDIKSAKRELKKARTVLQMDELKCRKRVLRRLGF
ATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFV
FQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFK
PHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKA
IGNTELENKFAEGITKIKRDIVFAASLYL
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain6ieh Chain B Residue 1102 [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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PDB6ieh NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.
Resolution2.892 Å
Binding residue
(original residue number in PDB)		F138 Q144 T163 S164 G166 K167 T168 K198 D252 R527
Binding residue
(residue number reindexed from 1)		F41 Q47 T66 S67 G69 K70 T71 K101 D155 R414
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ieh, PDBe:6ieh, PDBj:6ieh
PDBsum6ieh
PubMed30842217
UniProtP42285|MTREX_HUMAN Exosome RNA helicase MTR4 (Gene Name=MTREX)

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