Structure of PDB 8ka0 Chain C Binding Site BS01

Receptor Information
>8ka0 Chain C (length=405) Species: 672 (Vibrio vulnificus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESLVAARAEKVANLYRWLDTDNDVATDKYVPVPGFERVDVDVSDEVKQRM
IQSMSGYIEHTDNQVPKDQAEALATLFVESTLDYDWDKRVEFLTKLESYG
YSFEAPHAEKSIVSFWSGKNFKQYRDILDNAQTDGKKVVYDIDVKGNAFA
IDLNKHLMRWGGLFLDPDNAEQNQLKSSIDAATFSNTGFWSSVYATGAQN
DVYVIAEGGVRLGNYFWNVQLPALRQLQREGLVGEIRLLDKPVSEYKDLP
ADQIGRRLTDAGVAVKVRFDALSHERQAELLADNPDGYKADTLVELDVKL
SAIDSMLRESLPFYSLRTERNLLVQEGEEGFEVRSWPGIDGKSKTILLDN
PEDAAQQKSIERFILANFDNFEQMPDELFLVDNKVLSHHDGRTRIIAQKE
DGAWT
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain8ka0 Chain C Residue 2401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8ka0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+)
Resolution2.35 Å
Binding residue
(original residue number in PDB)		F2001 F2081 W2082 S2083 D2107 I2117 F2150 T2153 S2157 R2177 N2180 Y2181 F2182 Q2186 R2234
Binding residue
(residue number reindexed from 1)		F35 F115 W116 S117 D141 I151 F184 T187 S191 R211 N214 Y215 F216 Q220 R268
Annotation score2
External links
PDB RCSB:8ka0, PDBe:8ka0, PDBj:8ka0
PDBsum8ka0
PubMed39043696
UniProtA0A2S3R7M0|MARTX_VIBVL Multifunctional-autoprocessing repeats-in-toxin (Gene Name=CRN52_02910)

[Back to BioLiP]