Structure of PDB 1ib6 Chain D Binding Site BS03

Receptor Information
>1ib6 Chain D (length=312) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVAVLGAAGGIGQALALLLKTQLPSGSELSLYDIAPVTPGVAVDLSHIP
TAVKIKGFSGEDATPALEGADVVLISAGVARKPGMDRSDLFNVNAGIVKN
LVQQVAKTCPKACIGIITNPVNTTVAIAAEVLKKAGVYDKNKLFGVTTLD
IICSNTFVAELKGKQPGEVEVPVIGGHSGVTILPLLSQVPGVSFTEQEVA
DLTKRIQNAGTEVVEAKAGGGSATLSMGQAAARFGLSLVRALQGEQGVVE
CAYVEGDGQYARFFSQPLLLGKNGVEERKSIGTLSAFEQNALEGMLDTLK
KDIALGQEFVNK
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 chain1ib6 Chain D Residue 315 [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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PDB1ib6 Structural Analyses of a Malate Dehydrogenase with a Variable Active Site
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G10 G11 I12 Y33 D34 I35 S76 A77 G78 V79 A80 I97 I117 N119 H177 M227
Binding residue
(residue number reindexed from 1)		G10 G11 I12 Y33 D34 I35 S76 A77 G78 V79 A80 I97 I117 N119 H177 M227
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R87 D150 H177
Catalytic site (residue number reindexed from 1) R87 D150 H177
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016491 oxidoreductase activity
GO:0016615 malate dehydrogenase 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
GO:0042803 protein homodimerization activity
Biological Process
GO:0006096 glycolytic process
GO:0006099 tricarboxylic acid cycle
GO:0006108 malate metabolic process
GO:0006113 fermentation
GO:0009061 anaerobic respiration
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0019898 extrinsic component of membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ib6, PDBe:1ib6, PDBj:1ib6
PDBsum1ib6
PubMed11389141
UniProtP61889|MDH_ECOLI Malate dehydrogenase (Gene Name=mdh)

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