Structure of PDB 5cee Chain A Binding Site BS01

Receptor Information
>5cee Chain A (length=387) Species: 322098 (Aster yellows witches'-broom phytoplasma AYWB) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKEKALEMHEKNKGKVGVVSKVKVQNLDDLSLVYTPGVAEPCLKIKENPS
DVYRYTMKGNMVGVITNGTAVLGLGNIGPKASLPVMEGKAILFKELAGID
SFPICIDSTDSQEIVNIVSKISTVFGAINLEDIKSPQCIEIEDALKAKLD
IPVFHDDQHGTAIVVAAGILNALKVVKKSIEDVQVVINGAGSAGMAIAKM
LLLLKVNNVVLVDKTGTLYKGVANLNEPQKKLVEVTNKYQEKGTLKEVLK
GKDIFIGVSAPGIVTAEMVATMAKDAIVFALANPVPEIMPDEAKKGGARI
VATGRSDFPNQVNNCLAFPGVFRGTLDAKATQITEEMKKAATYALKNIIK
EQDLNENNILPTSFNKEVVKQIALAVCKVAKETGVVR
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 chain5cee Chain A Residue 401 [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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PDB5cee The crystal structure of the malic enzyme from Candidatus Phytoplasma reveals the minimal structural determinants for a malic enzyme.
Resolution2.498 Å
Binding residue
(original residue number in PDB)		T163 N190 G191 G193 A195 D215 K216 V260 S261 I265 L283 N285 V314 N316
Binding residue
(residue number reindexed from 1)		T161 N188 G189 G191 A193 D213 K214 V258 S259 I263 L281 N283 V312 N314
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y36 A72 K91 E133 D134 D158 D159 N285
Catalytic site (residue number reindexed from 1) Y34 A70 K89 E131 D132 D156 D157 N283
Enzyme Commision number 1.1.1.38: malate dehydrogenase (oxaloacetate-decarboxylating).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0004470 malic enzyme activity
GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity
GO:0008948 oxaloacetate decarboxylase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872 metal ion binding
GO:0051287 NAD binding

View graph for
Molecular Function
External links
PDB RCSB:5cee, PDBe:5cee, PDBj:5cee
PDBsum5cee
PubMed29652260
UniProtQ2NK75

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