Structure of PDB 6b5e Chain D Binding Site BS03

Receptor Information
>6b5e Chain D (length=286) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRGIILAGGSGTRLYPITMGISKQLLPVYDKPMIYYPLTTLMMAGIRDIQ
LITTPHDAPGFHRLLGDGAHLGVNISYATQDQPDGLAQAFVIGANHIGAD
SVALVLGDNIFYGPGLGTSLKRFQSISGGAIFAYWVANPSAYGVVEFGAE
GMALSLEEKPVTPKSNYAVPGLYFYDNDVIEIARGLKKSARGEYEITEVN
QVYLNQGRLAVEVLARGTAWLDTGTFDSLLDAADFVRTLERRQGLKVSIP
EEVAWRMGWIDDEQLVQRARALVKSGYGNYLLELLE
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain6b5e Chain D Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6b5e The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		M43 Y112 G113 P114 G115 G117 T118 S119 V247 E252 V253
Binding residue
(residue number reindexed from 1)		M43 Y112 G113 P114 G115 G117 T118 S119 V247 E252 V253
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.7.24: glucose-1-phosphate thymidylyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008879 glucose-1-phosphate thymidylyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006006 glucose metabolic process
GO:0009058 biosynthetic process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process
GO:0046075 dTTP metabolic process
Cellular Component
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6b5e, PDBe:6b5e, PDBj:6b5e
PDBsum6b5e
PubMed29076563
UniProtP9WH13|RMLA_MYCTU Glucose-1-phosphate thymidylyltransferase (Gene Name=rmlA)

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