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Structure of PDB 3okp Chain A Binding Site BS01

Receptor Information
>3okp Chain A (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 chain3okp Chain A Residue 601 [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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PDB3okp Acceptor substrate discrimination in phosphatidyl-myo-inositol mannoside synthesis: structural and mutational analysis of mannosyltransferase Corynebacterium glutamicum PimB'.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R206 K211 R260 L261 M266 I294 V295 E298
Binding residue
(residue number reindexed from 1)		R203 K208 R257 L258 M263 I291 V292 E295
Annotation score4
Binding affinityMOAD: Kd=19uM
PDBbind-CN: -logKd/Ki=4.72,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:3okp, PDBe:3okp, PDBj:3okp
PDBsum3okp
PubMed20843801
UniProtQ8NNK8|PIMB_CORGL GDP-mannose-dependent monoacylated alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase (Gene Name=pimB)

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