Structure of PDB 4dpm Chain D Binding Site BS01

Receptor Information
>4dpm Chain D (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 IDCOA
InChIInChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
InChIKeyRGJOEKWQDUBAIZ-IBOSZNHHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
ACDLabs 10.04O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC21 H36 N7 O16 P3 S
NameCOENZYME A
ChEMBLCHEMBL1213327
DrugBankDB01992
ZINCZINC000008551087
PDB chain4dpm Chain D Residue 402 [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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PDB4dpm Structural Basis for a Bispecific NADP+ and CoA Binding Site in an Archaeal Malonyl-Coenzyme A Reductase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G14 T16 G17 L18 G40 K41 G42 S43 P86 L87 N109 C153 G184 G186 Y187 N335
Binding residue
(residue number reindexed from 1)		G9 T11 G12 L13 G35 K36 G37 S38 P81 L82 N104 C148 G179 G181 Y182 N330
Annotation score3
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:4dpm, PDBe:4dpm, PDBj:4dpm
PDBsum4dpm
PubMed23325803
UniProtQ96YK1|MCR_SULTO Malonyl-CoA reductase (Gene Name=mcr)

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