Structure of PDB 3flk Chain D Binding Site BS02

Receptor Information
>3flk Chain D (length=359) Species: 303 (Pseudomonas putida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFRIAAIPGDGIGLEVLPEGIRVLEAAALKHGLALEFDTFEWASCDYYLQ
HGKMMPDDWAEQLKQYDAIYFGAVGWPDKVPDHISLWGSLLKFRREFDQY
VNIRPVRLFPGVPCALANRKVGDIDFVVVRENTEGEYSSLGGIMFENTEN
EIVIQESIFTRRGVDRILKYAFDLAEKRERKHVTSATKSNGMAISMPYWD
KRTEAMAAHYPHVSWDKQHIDILCARFVLQPERFDVVVASNLFGDILSDL
GPACAGTIGIAPSANLNPERNFPSLFEPVHGSAPDIFGKNIANPIAMIWS
GALMLEFLGQGDERYQRAHDDMLNAIERVIADGSVTPDMGGTLSTQQVGA
AISDTLARL
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain3flk 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]
PDB3flk Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		I16 A77 V78 G79 D86 L94 I263 H285 G286 S287 A288 D290 I291 A297 N298 D343
Binding residue
(residue number reindexed from 1)		I12 A73 V74 G75 D82 L90 I258 H280 G281 S282 A283 D285 I286 A292 N293 D338
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y141 K192 D225 D250 D254
Catalytic site (residue number reindexed from 1) Y137 K188 D221 D245 D249
Enzyme Commision number 1.1.1.83: D-malate dehydrogenase (decarboxylating).
1.1.1.93: tartrate dehydrogenase.
4.1.1.73: tartrate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0009027 tartrate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016829 lyase activity
GO:0046553 D-malate dehydrogenase (decarboxylating) (NAD+) activity
GO:0046872 metal ion binding
GO:0050319 tartrate decarboxylase activity
GO:0051287 NAD binding
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3flk, PDBe:3flk, PDBj:3flk
PDBsum3flk
PubMed20516620
UniProtQ51945|TTUC_PSEPU Tartrate dehydrogenase/decarboxylase

[Back to BioLiP]