Structure of PDB 3bk2 Chain A Binding Site BS03

Receptor Information
>3bk2 Chain A (length=549) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDHVEIIPLGGMGEIGKNITVFRFRDEIFVLDGGLAFPEEGMPGVDLLIP
RVDYLIEHRHKIKAWVLTHGHEDHIGGLPFLLPMIFGKESPVPIYGARLT
LGLLRGKLEEFGLRPGAFNLKEISPDDRIQVGRYFTLDLFRMTHSIPDNS
GVVIRTPIGTIVHTGDFKLDPTPIDGKVSHLAKVAQAGAEGVLLLIADAT
NAERPGYTPSEMEIAKELDRVIGRAPGRVFVTTFASHIHRIQSVIWAAEK
YGRKVAMEGRSMLKFSRIALELGYLKVKDRLYTLEEVKDLPDHQVLILAT
GSQGQPMSVLHRLAFEGHAKMAIKPGDTVILSSSPIPGNEEAVNRVINRL
YALGAYVLYPPTYKVHASGHASQEELKLILNLTTPRFFLPWHGEVRHQMN
FKWLAESMSRPPEKTLIGENGAVYRLTRETFEKVGEVPHGVLYVDGLGVG
DITEEILADRRHMAEEGLVVITALAGEDPVVEVVSRGFVKAGERLLGEVR
RMALEALKNGVREKKPLERIRDDIYYPVKKFLKKATGRDPMILPVVIEG
Ligand information
Ligand IDU5P
InChIInChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyDJJCXFVJDGTHFX-XVFCMESISA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
NameURIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL214393
DrugBankDB03685
ZINCZINC000002123545
PDB chain3bk2 Chain A Residue 950 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bk2 Structural insights into the dual activity of RNase J
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D79 F240 S340 P341 I342 P343 H372 S374
Binding residue
(residue number reindexed from 1)		D73 F234 S334 P335 I336 P337 H366 S368
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.-.-
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004519 endonuclease activity
GO:0004521 RNA endonuclease activity
GO:0004527 exonuclease activity
GO:0004534 5'-3' RNA exonuclease activity
GO:0008270 zinc ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006364 rRNA processing
GO:0006396 RNA processing
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:3bk2, PDBe:3bk2, PDBj:3bk2
PDBsum3bk2
PubMed18204464
UniProtQ72JJ7|RNJ_THET2 Ribonuclease J (Gene Name=rnj)

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