Structure of PDB 4req Chain A Binding Site BS02

Receptor Information
>4req Chain A (length=726) Species: 1752 (Propionibacterium freudenreichii subsp. shermanii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNE
DVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFY
RRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMREL
FAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILK
EFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATA
DIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLR
AARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEA
MAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDP
WSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAAR
TQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAE
RDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDAL
EKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILL
AKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVV
GVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAV
EIYTPGTVIPESAISLVKKLRASLDA
Ligand information
Ligand IDSCA
InChIInChI=1S/C25H40N7O19P3S/c1-25(2,20(38)23(39)28-6-5-14(33)27-7-8-55-16(36)4-3-15(34)35)10-48-54(45,46)51-53(43,44)47-9-13-19(50-52(40,41)42)18(37)24(49-13)32-12-31-17-21(26)29-11-30-22(17)32/h11-13,18-20,24,37-38H,3-10H2,1-2H3,(H,27,33)(H,28,39)(H,34,35)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t13-,18-,19-,20+,24-/m1/s1
InChIKeyVNOYUJKHFWYWIR-ITIYDSSPSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
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)NCCSC(=O)CCC(=O)O)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)NCCSC(=O)CCC(O)=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)NCCSC(=O)CCC(O)=O
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)NCCSC(=O)CCC(=O)O)O
FormulaC25 H40 N7 O19 P3 S
NameSUCCINYL-COENZYME A
ChEMBL
DrugBankDB03699
ZINCZINC000008551116
PDB chain4req Chain A Residue 801 [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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PDB4req Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y75 M78 F81 R82 T85 R87 Y89 S164 T166 T195 Q197 R207 N236 Y243 H244 R283 S285 F287 R326 H328 Q361
Binding residue
(residue number reindexed from 1)		Y73 M76 F79 R80 T83 R85 Y87 S162 T164 T193 Q195 R205 N234 Y241 H242 R281 S283 F285 R324 H326 Q359
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y89 Y243 H244 K604 D608 H610
Catalytic site (residue number reindexed from 1) Y87 Y241 H242 K602 D606 H608
Enzyme Commision number 5.4.99.2: methylmalonyl-CoA mutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004494 methylmalonyl-CoA mutase activity
GO:0005515 protein binding
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
Biological Process
GO:0019678 propionate metabolic process, methylmalonyl pathway
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4req, PDBe:4req, PDBj:4req
PDBsum4req
PubMed9655823
UniProtP11653|MUTB_PROFR Methylmalonyl-CoA mutase large subunit (Gene Name=mutB)

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