Structure of PDB 1mdt Chain B Binding Site BS01

Receptor Information
>1mdt Chain B (length=523) Species: 10703 (Corynephage beta) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDW
KGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAE
TIKKELGLSLTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYI
NNWEQAKALSVELEINFETRGKRGQDAMYEYMAQACASCINLDWDVIRDK
TKTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSE
LKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKTTAALSILPGIGS
VMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNFVE
SIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQG
ESGHDIKITAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCR
AIDGDVTFCRPKSPVYVGNGVHANLHVAFHRSSSEKIHSNEISSDSIGVL
GYQKTVDHTKVNSKLSLFFEIKS
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 chain1mdt Chain B Residue 901 [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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PDB1mdt Refined structure of monomeric diphtheria toxin at 2.3 A resolution.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		H21 G22 K24 Y27 I31 Q36 T42 G44 Y54 Y65 W153 S446 R458
Binding residue
(residue number reindexed from 1)		H21 G22 K24 Y27 I31 Q36 T42 G44 Y54 Y65 W153 S434 R446
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1mdt, PDBe:1mdt, PDBj:1mdt
PDBsum1mdt
PubMed7833808
UniProtP00588|DTX_CORBE Diphtheria toxin

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