Structure of PDB 5req Chain D Binding Site BS01

Receptor Information
>5req Chain D (length=619) Species: 1752 (Propionibacterium freudenreichii subsp. shermanii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKRLTVHTVDG
IDIVPMYRPKDAPKKLGYPGVAPFTRGTTVRNGDMDAWDVRALHEDPDEK
FTRKAILEGLERGVTSLLLRVDPDAIAPEHLDEVLSDVLLEMTKVEVFSR
YDQGAAAEALVSVYERSDKPAKDLALNLGLDPIGFAALQGTEPDLTVLGD
WVRRLAKFSPDSRAVTIDANIYHNAGAGDVAELAWALATGAEYVRALVEQ
GFTATEAFDTINFRVTATHDQFLTIARLRALREAWARIGEVFGVDEDKRG
ARQNAITSWRELTREDPYVNILRGSIATFSASVGGAESITTLPFTQALGL
PEDDFPLRIARNTGIVLAEEVNIGRVNDPAGGSYYVESLTRSLADAAWKE
FQEVEKLGGMSKAVMTEHVTKVLDACNAERAKRLANRKQPITAVSEFPMI
GARSIETKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLG
TRRDFGGREGFSSPVWHIAGIDTPQVEGGTTAEIVEAFKKSGAQVADLCS
SAKVYAQQGLEVAKALKAAGAKALYLSGAFKEFGDDAAEAEKLIDGRLFM
GMDVVDTLSSTLDILGVAK
Ligand information
Ligand IDMCD
InChIInChI=1S/C26H42N7O19P3/c1-13(25(39)40)14(34)5-4-7-28-16(35)6-8-29-23(38)20(37)26(2,3)10-49-55(46,47)52-54(44,45)48-9-15-19(51-53(41,42)43)18(36)24(50-15)33-12-32-17-21(27)30-11-31-22(17)33/h11-13,15,18-20,24,36-37H,4-10H2,1-3H3,(H,28,35)(H,29,38)(H,39,40)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/t13-,15+,18+,19+,20-,24+/m0/s1
InChIKeyNFOFXPNZJMTBQW-XSSXAYJJSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(C(=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)C
CACTVS 3.341C[C@H](C(O)=O)C(=O)CCCNC(=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 1.5.0CC(C(=O)CCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)C(=O)O
OpenEye OEToolkits 1.5.0C[C@@H](C(=O)CCCNC(=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)C(=O)O
CACTVS 3.341C[CH](C(O)=O)C(=O)CCCNC(=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
FormulaC26 H42 N7 O19 P3
NameMETHYLMALONYL(CARBADETHIA)-COENZYME A
ChEMBL
DrugBank
ZINCZINC000195757938
PDB chain5req Chain C Residue 2802 [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)		V42 R45
Binding residue
(residue number reindexed from 1)		V23 R26
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L112 N239 I240 E601 D605 A607
Catalytic site (residue number reindexed from 1) L93 N220 I221 E582 D586 A588
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:0019652 lactate fermentation to propionate and acetate
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
UniProtP11652|MUTA_PROFR Methylmalonyl-CoA mutase small subunit (Gene Name=mutA)

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