Structure of PDB 6zme Chain CI Binding Site BS05

Receptor Information
>6zme Chain CI (length=582) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISET
LCIGCGICIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPG
EVLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDWQEILTYFRGSELQ
NYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQ
LDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRL
KAAITIRSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPF
SVREGINIFLDGYVPTENLRFRDASLVFKMCMYKYPGMKKKMGEFELAIV
AGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQK
ISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGG
ELQRVALALCLGKPADVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTA
FVVEHDFIMATYLADRVIVFDGVPSKNTVANSPQTLLAGMNKFLSQLEIT
FRRDPNNYRPRINKLNSIKDVEQKKSGNYFFL
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 chain6zme Chain CI Residue 603 [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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PDB6zme Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Y87 G113 I114 G115 K116 S117
Binding residue
(residue number reindexed from 1)		Y84 G110 I111 G112 K113 S114
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017111 ribonucleoside triphosphate phosphatase activity
GO:0043024 ribosomal small subunit binding
GO:0043273 CTPase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0060698 endoribonuclease inhibitor activity
Biological Process
GO:0000054 ribosomal subunit export from nucleus
GO:0006413 translational initiation
GO:0006415 translational termination
GO:0006417 regulation of translation
GO:0032790 ribosome disassembly
GO:0060702 negative regulation of endoribonuclease activity
GO:0072344 rescue of stalled ribosome
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0016020 membrane
GO:0022626 cytosolic ribosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6zme, PDBe:6zme, PDBj:6zme
PDBsum6zme
PubMed32680882
UniProtP61221|ABCE1_HUMAN ATP-binding cassette sub-family E member 1 (Gene Name=ABCE1)

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