Structure of PDB 5u32 Chain A Binding Site BS01

Receptor Information
>5u32 Chain A (length=213) Species: 237561 (Candida albicans SC5314) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSTTTKYIFVPIATIGCGKTTVFNTLNNLFPQWTHIQNDNISKKAKLKIC
DLTLLALEDDDQSVVLFDRNNSASRERRQIFTTIDQKRDEHLDDTVDLKY
IAINFIPEDLSEEELWDITYNRVIQLDENLVESVMKGFIQRYQPINTSRS
PDDQFDHVIHLKLSKDENSSKSSLENVRIIIDDLVQNFPDLIKEKPADEL
INECFQKALDYKP
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5u32 Chain A Residue 701 [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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PDB5u32 Structural basis for the GTP specificity of the RNA kinase domain of fungal tRNA ligase.
Resolution2.191 Å
Binding residue
(original residue number in PDB)		G422 G424 K425 T426 T427 R528 D583 K588 S589 S590
Binding residue
(residue number reindexed from 1)		G16 G18 K19 T20 T21 R122 D166 K171 S172 S173
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.3: RNA ligase (ATP).
Gene Ontology
Molecular Function
GO:0003972 RNA ligase (ATP) activity
GO:0005524 ATP binding
Biological Process
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation

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Molecular Function
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Biological Process
External links
PDB RCSB:5u32, PDBe:5u32, PDBj:5u32
PDBsum5u32
PubMed29165709
UniProtP43075|TRNL_CANAL tRNA ligase (Gene Name=LIG1)

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