Structure of PDB 4req Chain C Binding Site BS03

Receptor Information
>4req Chain C (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 IDMCA
InChIInChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-13,16-18,22,34-35H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t12-,13-,16-,17-,18+,22-/m1/s1
InChIKeyMZFOKIKEPGUZEN-AGCMQPJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[CH](C(O)=O)C(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(O)C(C(=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)C
CACTVS 3.341C[C@H](C(O)=O)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O
OpenEye OEToolkits 1.5.0CC(C(=O)O)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
FormulaC25 H40 N7 O19 P3 S
NameMETHYLMALONYL-COENZYME A
ChEMBL
DrugBankDB04045
ZINCZINC000008551337
PDB chain4req Chain C Residue 802 [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 T77 M78 F81 R82 T85 R87 Y89 S114 S164 T166 T195 R207 N236 Y243 H244 R283 S285 F287 T327 H328 Q361 S362
Binding residue
(residue number reindexed from 1)		Y73 T75 M76 F79 R80 T83 R85 Y87 S112 S162 T164 T193 R205 N234 Y241 H242 R281 S283 F285 T325 H326 Q359 S360
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

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Molecular Function
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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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