Structure of PDB 5trd Chain B Binding Site BS03

Receptor Information
>5trd Chain B (length=215) Species: 273075 (Thermoplasma acidophilum DSM 1728) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYIT
RTVTKRGQILNITEKGLDVLYTEFADLSRILAIKNNVVITGTVTSGMGEG
RYYVARKQYIIQFQEKLGIIPYLGTLNIKVDQASLPELRKIRGFRGIHIE
GFKTEDRTFGSVKAFPAKIQNIPCFVIMPERTVYTDVIEIISDKYLREEI
NLHDGDRVSVEVYTE
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain5trd Chain B Residue 301 [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]
PDB5trd Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator
Resolution1.85 Å
Binding residue
(original residue number in PDB)		G102 M103 G104 E105 G106 R107 Y128 G130 T131 L132 N133 Y201 L202 R203
Binding residue
(residue number reindexed from 1)		G96 M97 G98 E99 G100 R101 Y122 G124 T125 L126 N127 Y195 L196 R197
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.1.161: CTP-dependent riboflavin kinase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0008531 riboflavin kinase activity
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0046872 metal ion binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0009231 riboflavin biosynthetic process
GO:0009398 FMN biosynthetic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5trd, PDBe:5trd, PDBj:5trd
PDBsum5trd
PubMed
UniProtQ9HJA6|RIFK_THEAC Riboflavin kinase (Gene Name=ribK)

[Back to BioLiP]