Structure of PDB 3oka Chain B Binding Site BS01

Receptor Information
>3oka Chain B (length=378) Species: 1718 (Corynebacterium glutamicum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRKTLVVTNDFPPRIGGIQSYLRDFIATQDPESIVVFASTQNAEEAHAYD
KTLDYEVIRWPRSVMLPTPTTAHAMAEIIREREIDNVWFGAAAPLALMAG
TAKQAGASKVIASTHGHEVGWSMLPGSRQSLRKIGTEVDVLTYISQYTLR
RFKSAFGSHPTFEHLPSGVDVKRFTPATPEDKSATRKKLGFTDTTPVIAC
NSRLVPRKGQDSLIKAMPQVIAARPDAQLLIVGSGRYESTLRRLATDVSQ
NVKFLGRLEYQDMINTLAAADIFAMPARTRGGGLDVEGLGIVYLEAQACG
VPVIAGTSGGAPETVTPATGLVVEGSDVDKLSELLIELLDDPIRRAAMGA
AGRAHVEAEWSWEIMGERLTNILQSEPR
Ligand information
Ligand IDGDD
InChIInChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKeyMVMSCBBUIHUTGJ-GDJBGNAASA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC16 H25 N5 O16 P2
NameGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
ChEMBL
DrugBank
ZINCZINC000008215581
PDB chain3oka Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3oka Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB'.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R206 K211 R260 L261 M266 E298
Binding residue
(residue number reindexed from 1)		R203 K208 R257 L258 M263 E295
Annotation score4
Binding affinityMOAD: Kd=19uM
Enzymatic activity
Enzyme Commision number 2.4.1.346: phosphatidyl-myo-inositol dimannoside synthase.
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
GO:0033164 glycolipid 1,6-alpha-mannosyltransferase activity
GO:0043750 phosphatidylinositol alpha-mannosyltransferase activity
Biological Process
GO:0008654 phospholipid biosynthetic process
GO:0009247 glycolipid biosynthetic process
GO:0046488 phosphatidylinositol metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3oka, PDBe:3oka, PDBj:3oka
PDBsum3oka
PubMed20843801
UniProtQ8NNK8|PIMB_CORGL GDP-mannose-dependent monoacylated alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase (Gene Name=pimB)

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