Structure of PDB 5ujk Chain A Binding Site BS01

Receptor Information
>5ujk Chain A (length=315) Species: 408 (Methylorubrum extorquens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARSKIALIGAGQIGGTLAHLAGLKELGDVVLFDIVDGVPQGKALDIAESA
PVDGFDAKYSGASDYSAIAGADVVIVTAGVPRKPGMSRDDLIGINLKVME
AVGAGIKEHAPDAFVICITNPLDAMVWALQKFSGLPTNKVVGMAGVLDSA
RFRHFLAEEFGVSVEDVTAFVLGGHGDDMVPLTRYSTVAGVPLTDLVKLG
WTTQEKLDAMVERTRKGGGEIVNLLKTGSAFYAPAASAIAMAESYLRDKK
RVLPCAAYLDGQYGIDGLYVGVPVVIGENGVERVLEVTFNDDEKAMFEKS
VNSVKGLIEACKSVN
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 chain5ujk 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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PDB5ujk Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase.
Resolution1.53 Å
Binding residue
(original residue number in PDB)		G12 Q13 I14 D34 I35 T78 A79 G80 V99 I119 N121 M144 L148 H176
Binding residue
(residue number reindexed from 1)		G11 Q12 I13 D33 I34 T77 A78 G79 V98 I118 N120 M143 L147 H175
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R89 D149 R152 H176
Catalytic site (residue number reindexed from 1) R88 D148 R151 H175
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004459 L-lactate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0030060 L-malate dehydrogenase (NAD+) activity
Biological Process
GO:0006089 lactate metabolic process
GO:0006090 pyruvate metabolic process
GO:0006099 tricarboxylic acid cycle
GO:0019752 carboxylic acid metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ujk, PDBe:5ujk, PDBj:5ujk
PDBsum5ujk
PubMed30279311
UniProtQ84FY8|MDH_METEA Malate dehydrogenase (Gene Name=mdh)

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