Structure of PDB 5y37 Chain B Binding Site BS01

Receptor Information
>5y37 Chain B (length=339) Species: 211110 (Streptococcus agalactiae NEM316) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVDMVVKVGINGFGRIGRLAFRRIQNVEGVEVTRINDLTDPNMLAHLLKY
DTTQGRFDGTVEVKEGGFEVNGQFVKVSAEREPANIDWATDGVEIVLEAT
GFFASKEKAEQHIHENGAKKVVITAPGGNDVKTVVFNTNHDILDGTETVI
SGASCTTNCLAPMAKALQDNFGVKQGLMTTIHAYTGDQMILDGPHRGGDL
RRARAGAANIVPNSTGAAKAIGLVIPELNGKLDGAAQRVPVPTGSVTELV
ATLEKDVTVEEVNAAMKAAANDSYGYTEDPIVSSDIVGISYGSLFDATQT
KVQTVDGNQLVKVVSWYDNEMSYTSQLVRTLEYFAKIAK
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 chain5y37 Chain B Residue 401 [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]
PDB5y37 High-resolution crystal structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase.
Resolution1.36 Å
Binding residue
(original residue number in PDB)		G13 G15 R16 I17 D38 L39 A100 T101 G102 F103 F104 T125 C156 N320 Y324
Binding residue
(residue number reindexed from 1)		G12 G14 R15 I16 D37 L38 A99 T100 G101 F102 F103 T124 C155 N319 Y323
Annotation score4
Enzymatic activity
Enzyme Commision number 1.2.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006006 glucose metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5y37, PDBe:5y37, PDBj:5y37
PDBsum5y37
PubMed29633972
UniProtQ8E3E8

[Back to BioLiP]