Structure of PDB 1f0l Chain A Binding Site BS01

Receptor Information
>1f0l Chain A (length=520) Species: 1717 (Corynebacterium diphtheriae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDW
KGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAE
TIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYI
NNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACACINLDWDVIRDKT
KTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSEL
KTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGSV
MGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELIGFAAYNFVESII
NLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESG
HDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAID
GDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQ
KTVDHTKVNSKLSLFFEIKS
Ligand information
Ligand IDAPU
InChIInChI=1S/C19H25N7O15P2/c20-15-10-16(22-5-21-15)26(6-23-10)18-11(29)13(7(3-27)38-18)41-43(35,36)37-4-8-14(40-42(32,33)34)12(30)17(39-8)25-2-1-9(28)24-19(25)31/h1-2,5-8,11-14,17-18,27,29-30H,3-4H2,(H,35,36)(H2,20,21,22)(H,24,28,31)(H2,32,33,34)/t7-,8-,11-,12-,13-,14-,17-,18-/m1/s1
InChIKeyFZCSEXOMUJFOHQ-KPKSGTNCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O[P](O)(O)=O)N5C=CC(=O)NC5=O)[C@H]3O
ACDLabs 10.04O=C1C=CN(C(=O)N1)C2OC(C(OP(=O)(O)O)C2O)COP(=O)(O)OC5C(OC(n4cnc3c(ncnc34)N)C5O)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CC(=O)NC5=O)O)OP(=O)(O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OCC4C(C(C(O4)N5C=CC(=O)NC5=O)O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O[P](O)(O)=O)N5C=CC(=O)NC5=O)[CH]3O
FormulaC19 H25 N7 O15 P2
NameADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE
ChEMBL
DrugBankDB01792
ZINCZINC000024469737
PDB chain1f0l 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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PDB1f0l Characterization of High-Order Oligomerization and Energetics in Diphtheria Toxin
Resolution1.55 Å
Binding residue
(original residue number in PDB)		H21 G22 K24 Y27 I31 I35 Q36 T42 G44 F53 Y54 Y65 W153 S446 R458
Binding residue
(residue number reindexed from 1)		H21 G22 K24 Y27 I31 I35 Q36 T42 G44 F53 Y54 Y65 W153 S431 R443
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) E148
Catalytic site (residue number reindexed from 1) E148
Enzyme Commision number 2.4.2.36: NAD(+)--diphthamide ADP-ribosyltransferase.
Gene Ontology
Molecular Function
GO:0008320 protein transmembrane transporter activity
GO:0016757 glycosyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0042802 identical protein binding
GO:0047286 NAD+-diphthamide ADP-ribosyltransferase activity
GO:0090729 toxin activity
Biological Process
GO:0035821 modulation of process of another organism
GO:0071806 protein transmembrane transport
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1f0l, PDBe:1f0l, PDBj:1f0l
PDBsum1f0l
PubMed
UniProtP00588|DTX_CORBE Diphtheria toxin

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