Structure of PDB 4dwr Chain C Binding Site BS02

Receptor Information
>4dwr Chain C (length=481) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVA
MLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVR
LIRTNLTEKEVRPRIKQLVDTLFKNVPSGVRIKLHWTQIDDVLVDGAKWA
VDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSGNHFL
EVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRIMERA
IRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITHWVRE
SFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRKGATR
AFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGSTCHG
AGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAYKNVD
NVVKVVSEAGIAKLVARMRPIGVAKGAAALE
Ligand information
Ligand IDFRU
InChIInChI=1S/C6H12O6/c7-1-3-4(9)5(10)6(11,2-8)12-3/h3-5,7-11H,1-2H2/t3-,4-,5+,6-/m1/s1
InChIKeyRFSUNEUAIZKAJO-ARQDHWQXSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04OC1C(O)C(OC1(O)CO)CO
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O
CACTVS 3.341OC[CH]1O[C](O)(CO)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)(CO)O)O)O)O
CACTVS 3.341OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O
FormulaC6 H12 O6
Namebeta-D-fructofuranose;
beta-D-fructose;
D-fructose;
fructose
ChEMBLCHEMBL604608
DrugBank
ZINCZINC000001529270
PDB chain4dwr Chain F Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dwr Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH.
Resolution1.48 Å
Binding residue
(original residue number in PDB)		Y57 K58 D340
Binding residue
(residue number reindexed from 1)		Y56 K57 D335
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.-.-
6.5.1.8: 3'-phosphate/5'-hydroxy nucleic acid ligase.
Gene Ontology
Molecular Function
GO:0008452 RNA ligase activity
Biological Process
GO:0006396 RNA processing

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Molecular Function
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Biological Process
External links
PDB RCSB:4dwr, PDBe:4dwr, PDBj:4dwr
PDBsum4dwr
PubMed22949672
UniProtO59245|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)

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