Structure of PDB 2dbz Chain A Binding Site BS01

Receptor Information
>2dbz Chain A (length=333) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKPKVFITREIPEVGIKMLEDEFEVEVWGDEKEIPREILLKKVKEVDALV
TMLSERIDKEVFENAPKLRIVANYAVGYDNIDIEEATKRGIYVTNTPDVL
TDATADLAFALLLATARHVVKGDRFVRSGEWKKRGVAWHPKWFLGYDVYG
KTIGIIGLGRIGQAIAKRAKGFNMRILYYSRTRKEEVERELNAEFKPLED
LLRESDFVVLAVPLTRETYHLINEERLKLMKKTAILINIARGKVVDTNAL
VKALKEGWIAGAGLDVFEEEPYYNEELFKLDNVVLTPHIGSASFGAREGM
AELVAKNLIAFKRGEIPPTLVNREVIKIRKPGF
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)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[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]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)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain2dbz Chain A 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]
PDB2dbz Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		V76 T104 G157 G159 R160 I161 S180 R181 A211 P213 T218 I239 A240 R241 D265 H288 G290
Binding residue
(residue number reindexed from 1)		V76 T104 G157 G159 R160 I161 S180 R181 A211 P213 T218 I239 A240 R241 D265 H288 G290
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L100 R241 D265 E270 H288
Catalytic site (residue number reindexed from 1) L100 R241 D265 E270 H288
Enzyme Commision number 1.1.1.26: glyoxylate reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016618 hydroxypyruvate reductase [NAD(P)H] activity
GO:0030267 glyoxylate reductase (NADPH) activity
GO:0047964 glyoxylate reductase (NADH) activity
GO:0051287 NAD binding
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:2dbz, PDBe:2dbz, PDBj:2dbz
PDBsum2dbz
PubMed17327673
UniProtO58320|GYAR_PYRHO Glyoxylate reductase (Gene Name=gyaR)

[Back to BioLiP]