Structure of PDB 5ddk Chain B Binding Site BS01

Receptor Information
>5ddk Chain B (length=504) Species: 1457393 (Acetobacter aceti 1023) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TERIRNVALRSKVCPAETASELIKHGDVVGTSGFTGAGYPKEVPKALAQR
MEAAHDRGEKYQISLITGASTGPQLDGELAKANGVYFRSPFNTDATMRNR
INAGETEYFDNHLGQVAGRAVQGNYGKFNIALVEATAITEDGGIVPTSSV
GNSQTFLNLAEKVIIEVNEWQNPMLEGIHDIWDGNVSGVPTRDIVPIVRA
DQRVGGPVLRVNPDKIAAIVRTNDRDRNAPFAAPDETAKAIAGYLLDFFG
HEVKQNRLPPSLLPLQSGVGNVANAVLEGLKEGPFENLVGYSEVIQDGML
AMLDSGRMRIASASSFSLSPEAAEEINNRMDFFRSKIILRQQDVSASPGI
IRRLGCIAMNGMIEADIYGNVNSTRVMGSKMMNGIGGSGDFARSSYLSIF
LSPSTAKGGKISAIVPMAAHVDHIMQDAQIFVTEQGLADLRGLSPVQRAR
EIISKCAHPDYRPMLQDYFDRALKNSFGKHTPHLLTEALSWHQRFIDTGT
MLPS
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 chain5ddk Chain B Residue 603 [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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PDB5ddk Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase.
Resolution2.127 Å
Binding residue
(original residue number in PDB)		G269 V270 G271 N272 V273 E294 M363 I364 N384 G385 S389 A407 K408 I412
Binding residue
(residue number reindexed from 1)		G268 V269 G270 N271 V272 E293 M362 I363 N383 G384 S388 A406 K407 I411
Annotation score3
Enzymatic activity
Enzyme Commision number 2.8.3.18: succinyl-CoA:acetate CoA-transferase.
Gene Ontology
Molecular Function
GO:0003986 acetyl-CoA hydrolase activity
GO:0008410 CoA-transferase activity
GO:0008775 acetate CoA-transferase activity
GO:0016740 transferase activity
Biological Process
GO:0006083 acetate metabolic process
GO:0006084 acetyl-CoA metabolic process
GO:0006085 acetyl-CoA biosynthetic process
GO:0019427 acetyl-CoA biosynthetic process from acetate
GO:0045733 acetate catabolic process
GO:1901289 succinyl-CoA catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ddk, PDBe:5ddk, PDBj:5ddk
PDBsum5ddk
PubMed27242998
UniProtB3EY95|SCACT_ACEAC Succinyl-CoA:acetate CoA-transferase

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