Structure of PDB 4dpl Chain B Binding Site BS01

Receptor Information
>4dpl Chain B (length=354) Species: 273063 (Sulfurisphaera tokodaii str. 7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTLKAAILGATGLVGIEYVRMLSNHPYIKPAYLAGKGSVGKPYGEVVRWQ
TVGQVPKEIADMEIKPTDPKLMDDVDIIFSPLPQGAAGPVEEQFAKEGFP
VISNSPDHRFDPDVPLLVPELNPHTISLIDEQRKRREWKGFIVTTPLCTA
QGAAIPLGAIFKDYKMDGAFITTIQSLSGAGYPGIPSLDVVDNILPLGDG
YDAKTIKEIFRILSEVKRNVDEPKLEDVSLAATTHRIATIHGHYEVLYVS
FKEETAAEKVKETLENFRGEPQDLKLPTAPSKPIIVMNEDTRPQVYFDRW
AGDIPGMSVVVGRLKQVNKRMIRLVSLIHNTVRGAAGGGILAAELLVEKG
YIEK
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 chain4dpl 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

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PDB4dpl Structural Basis for a Bispecific NADP+ and CoA Binding Site in an Archaeal Malonyl-Coenzyme A Reductase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G14 T16 G17 L18 V19 K41 G42 P86 L87 P88 N109 C153 G184 G186 Y187 N335 T336 G339 A340
Binding residue
(residue number reindexed from 1)		G9 T11 G12 L13 V14 K36 G37 P81 L82 P83 N104 C148 G179 G181 Y182 N330 T331 G334 A335
Annotation score4
Enzymatic activity
Enzyme Commision number 1.2.1.75: malonyl CoA reductase (malonate semialdehyde-forming).
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004073 aspartate-semialdehyde dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0046983 protein dimerization activity
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0009086 methionine biosynthetic process
GO:0009088 threonine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4dpl, PDBe:4dpl, PDBj:4dpl
PDBsum4dpl
PubMed23325803
UniProtQ96YK1|MCR_SULTO Malonyl-CoA reductase (Gene Name=mcr)

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