Structure of PDB 4xwt Chain B Binding Site BS04

Receptor Information
>4xwt Chain B (length=543) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APTLEVIPLGGMGEIGKNITVFRYGDEIVVVDGGLAFPKAHQMGIDLIVP
RIDYLLEHQDKIKGWILTHGHEDHIGGLPYIFARLPRVPVYGLPLTLALV
REKLSEFGLQDVDLREVTYGDEVRFGQSFVAEFFCMTHSIPDNAGYILKT
PVGDVLHTGDFKIDPDVGTGAGIVSDLERVEQAGKDGVLLLISDSTNAER
PGHTPSEAEIARNLEEIIKGCRGRVFLTTFASQVYRIQNILDLAHRQGRR
VVMEGRSMIKYAQAAQATGHMNPPEPFLTSEEVGELQDQQVLFVCTGSQG
QPMAVLGRLAFGTHAKIALRRGDTVILSSNPIPGNEDAVNLIVNRLYEIG
VDVVYPPTYRVHASGHASQEELATILNLTRPKFFLPWHGEPRHQINHAKL
AQTLPRPPKRTLIAKNGDIVNLGPDEFRVSGTVAAGAVYVDGLGVGDVND
DVLLDRVNLSQEGLLILTAVLHPTPHVEVVARGFARPNRDLELQIRRVAL
EAVEQGLREKKRLEDVRDDMYGAVRRFTRKATGRNPVLIPMIV
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 chain4xwt Chain B Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xwt Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J
Resolution2.003 Å
Binding residue
(original residue number in PDB)		S154 T211 S379 G380 H381
Binding residue
(residue number reindexed from 1)		S139 T196 S364 G365 H366
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: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:4xwt, PDBe:4xwt, PDBj:4xwt
PDBsum4xwt
PubMed25940620
UniProtH9CZL7

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