Structure of PDB 6b5e Chain D Binding Site BS01

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 IDDAU
InChIInChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1
InChIKeyYSYKRGRSMLTJNL-URARBOGNSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O
ACDLabs 12.01O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O)C
FormulaC16 H26 N2 O16 P2
Name2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
ChEMBLCHEMBL412989
DrugBankDB03751
ZINC
PDB chain6b5e Chain D 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]
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)		L6 G8 Q24 Q80 P83 G85 L86 L106 D108 G143 E158 K159 V169 W220 D222
Binding residue
(residue number reindexed from 1)		L6 G8 Q24 Q80 P83 G85 L86 L106 D108 G143 E158 K159 V169 W220 D222
Annotation score4
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

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

[Back to BioLiP]