Structure of PDB 6tzm Chain A Binding Site BS01

Receptor Information
>6tzm Chain A (length=211) Species: 237561 (Candida albicans SC5314) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STTTKYIFVPIATIGCGKTTVFNTLNNLFPQWTHIQNDNISKKAKLKICD
LTLLALEDDDQSVVLFDRNNSASRERRQIFTTIDQKRDEHLDDTVDLKYI
AINFIPEDLSEEELWDITYNRVIQLDENLVESVMKGFIQRYQPINTSRSP
DDQFDHVIHLKLSKDENSLKSSLENVRIIIDDLVQNFPDLIKEKPADELI
NECFQKALDYK
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 chain6tzm Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6tzm Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Resolution1.714 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)		G15 G17 K18 T19 T20 R121 D165 K170 S171 S172
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6tzm, PDBe:6tzm, PDBj:6tzm
PDBsum6tzm
PubMed31722405
UniProtP43075|TRNL_CANAL tRNA ligase (Gene Name=LIG1)

[Back to BioLiP]