Structure of PDB 4iym Chain O Binding Site BS01

Receptor Information
>4iym Chain O (length=489) Species: 266834 (Sinorhizobium meliloti 1021) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVES
AKAAQPKWAATNPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAK
GDIVRGLEVCEFVIGIPHLQKSEFTEGAGPGIDMYSIRQPVGIGAGITPF
NFPGMIPMWMFAPAIACGNAFILKPSERDPSVPIRLAELMIEAGLPAGIL
NVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNGKRAQCFGG
AKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLI
DKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVV
DGRDFKLQGYENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEE
ALSLPMKHEYGNGVAIYTRDGDAARDFASRINIGMVGVNVPIPVPLAYHS
FGGWKSSSFGDLNQHGTDSIKFWTRTKTITSRWPSGIKD
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 chain4iym Chain O Residue 501 [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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PDB4iym Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934
Resolution2.2 Å
Binding residue
(original residue number in PDB)		T145 P146 F147 N148 F149 K171 E174 K204 V207 F221 V222 G223 S224 I227 R278 C279 E381 F383
Binding residue
(residue number reindexed from 1)		T148 P149 F150 N151 F152 K174 E177 K207 V210 F224 V225 G226 S227 I230 R281 C282 E384 F386
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) N148 K171 F245 C279 E381 Q461
Catalytic site (residue number reindexed from 1) N151 K174 F248 C282 E384 Q464
Enzyme Commision number 1.2.1.27: methylmalonate-semialdehyde dehydrogenase (CoA acylating).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004491 methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0018478 malonate-semialdehyde dehydrogenase (acetylating) activity
Biological Process
GO:0006210 thymine catabolic process
GO:0006574 valine catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4iym, PDBe:4iym, PDBj:4iym
PDBsum4iym
PubMed
UniProtQ92RW4

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