Structure of PDB 2xzl Chain A Binding Site BS05

Receptor Information
>2xzl Chain A (length=756) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSL
HPDSDLGDTVLECYNCGRKNVFLLGFVSVVLLCRIPCAQTKWDTDQWQPL
IEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATIPPLLL
RYQDAYEYQRSYGPLIKLEADYDKQLKESQEHISVSWSLALNNRHLASFT
KVAIGDEMILWYSGMQHPDWEGRGYIVRLPNDTFTLELKPSKTPPPTHLT
TGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFD
VPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIV
YHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSV
SNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEIL
NKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVI
LVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYL
SEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEIS
ANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQ
MNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRR
LNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQL
CTVQLV
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 chain2xzl Chain A Residue 1854 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xzl Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Q408 Q413 G433 T434 G435 K436 T437 V438 Y638 R639 E769
Binding residue
(residue number reindexed from 1)		Q314 Q319 G339 T340 G341 K342 T343 V344 Y544 R545 E675
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2xzl, PDBe:2xzl, PDBj:2xzl
PDBsum2xzl
PubMed21419344
UniProtP30771|RENT1_YEAST ATP-dependent helicase NAM7 (Gene Name=NAM7)

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