Structure of PDB 5ld5 Chain D Binding Site BS01

Receptor Information
>5ld5 Chain D (length=340) Species: 525256 (Fannyhessea vaginae DSM 15829) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAVKVAINGFGRIGRLAFRQMFGHEGSEIVAINDLTDPKMLANLLKYDSS
QGNYARNHSVVAGEDSITVDGKTIKIYKEADAHNLPWGELNVDVVLECTG
FYTSKAKAQAHIDAGAKKVVISAPAGKDLPTIVYNVNHEILTKDDNIISA
ASCTTNCLAPMAKALNDFAPIQSGIMSTIHAFTGDQMVLDGPHRKGDLRR
ARAAAINIVPNSTGAAKAIGLVIPELNGKLIGSAQRVPVPTGSTTLLFAV
VKSDKEITVDSINAAMKAASDPETFGYNEDPIVSSDIIGMTYGSLFDATQ
TMVQDLGNGLYQVEVVSWYDNENSYTSQMVRTIKYFEKFV
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 chain5ld5 Chain D 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]
PDB5ld5 Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin.
Resolution2.1906 Å
Binding residue
(original residue number in PDB)		G26 R27 I28 D49 L50 T114 G115 F116 S137 C168 N336 Y340
Binding residue
(residue number reindexed from 1)		G11 R12 I13 D34 L35 T99 G100 F101 S122 C153 N321 Y325
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C168 H195
Catalytic site (residue number reindexed from 1) C153 H180
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:5ld5, PDBe:5ld5, PDBj:5ld5
PDBsum5ld5
PubMed28443070
UniProtF1T6A5

[Back to BioLiP]