Structure of PDB 5req Chain C Binding Site BS01

Receptor Information
>5req Chain C (length=725) Species: 1752 (Propionibacterium freudenreichii subsp. shermanii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNED
VYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQFAGFSTAKESNAFYR
RNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELF
AGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKE
FMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATAD
IEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRA
ARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAM
AATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPW
SGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAART
QARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAER
DPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALE
KVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLA
KMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVG
VSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVE
IYTPGTVIPESAISLVKKLRASLDA
Ligand information
Ligand IDSCD
InChIInChI=1S/C26H42N7O19P3/c1-26(2,21(39)24(40)29-9-7-16(35)28-8-3-4-14(34)5-6-17(36)37)11-49-55(46,47)52-54(44,45)48-10-15-20(51-53(41,42)43)19(38)25(50-15)33-13-32-18-22(27)30-12-31-23(18)33/h12-13,15,19-21,25,38-39H,3-11H2,1-2H3,(H,28,35)(H,29,40)(H,36,37)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/t15-,19-,20-,21+,25-/m1/s1
InChIKeyWPCFLGXXWJIJOV-ZMHDXICWSA-N
SMILES
SoftwareSMILES
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)NCCCC(=O)CCC(=O)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)NCCCC(=O)CCC(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)NCCCC(=O)CCC(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)NCCCC(=O)CCC(=O)O)O
ACDLabs 10.04O=C(O)CCC(=O)CCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC26 H42 N7 O19 P3
NameSUCCINYL(CARBADETHIA)-COENZYME A
ChEMBL
DrugBank
ZINCZINC000195757936
PDB chain5req Chain C Residue 2801 [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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PDB5req Stabilization of radical intermediates by an active-site tyrosine residue in methylmalonyl-CoA mutase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y75 T77 M78 F81 R82 T85 R87 F89 S164 T166 T195 R207 N236 Y243 H244 R283 S285 F287 H328 Q330 Q361 S362
Binding residue
(residue number reindexed from 1)		Y72 T74 M75 F78 R79 T82 R84 F86 S161 T163 T192 R204 N233 Y240 H241 R280 S282 F284 H325 Q327 Q358 S359
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) F89 Y243 H244 K604 D608 H610
Catalytic site (residue number reindexed from 1) F86 Y240 H241 K601 D605 H607
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:5req, PDBe:5req, PDBj:5req
PDBsum5req
PubMed9772164
UniProtP11653|MUTB_PROFR Methylmalonyl-CoA mutase large subunit (Gene Name=mutB)

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