Structure of PDB 6ime Chain B

Receptor sequence
>6imeB (length=285) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence]
NFPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPR
IPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELG
IKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVG
SRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIARE
VAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAY
AEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA
3D structure
PDB6ime Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.
ChainB
Resolution1.55 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 2.5.1.86: trans,polycis-decaprenyl diphosphate synthase.
2.5.1.87: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific].
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 CO3 B W125 R165 W114 R154
BS02 GST B M75 D76 G77 N78 G79 R80 R89 H93 G96 A119 R127 W271 M64 D65 G66 N67 G68 R69 R78 H82 G85 A108 R116 W260
BS03 ISY B V74 D76 Y118 A119 F120 R244 R250 S252 V63 D65 Y107 A108 F109 R233 R239 S241
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004659 prenyltransferase activity
GO:0008834 di-trans,poly-cis-undecaprenyl-diphosphate synthase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0030145 manganese ion binding
GO:0033850 Z-farnesyl diphosphate synthase activity
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
GO:0052923 all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity
Biological Process
GO:0016094 polyprenol biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ime, PDBe:6ime, PDBj:6ime
PDBsum6ime
PubMed30950820
UniProtP9WFF7|DPDS_MYCTU Decaprenyl diphosphate synthase (Gene Name=uppS)

[Back to BioLiP]