Structure of PDB 5obp Chain B Binding Site BS03

Receptor Information
>5obp Chain B (length=418) Species: 66821 (Sulfurospirillum multivorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPWF
LSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIYP
NRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGAD
LVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETDD
ELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWLC
QFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRLT
KVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSIH
NQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKNITEVWDGKINTY
GLDADHFRDTVSFRKDRV
Ligand information
Ligand ID9QQ
InChIInChI=1S/C59H84N13O15P.Co/c1-28-47-32(11-15-41(61)76)55(3,4)39(69-47)23-36-31(10-14-40(60)75)57(6,24-44(64)79)52(68-36)29(2)48-33(12-16-42(62)77)58(7,25-45(65)80)59(8,71-48)53-34(22-43(63)78)56(5,51(28)70-53)18-17-46(81)66-19-20-85-88(83,84)87-50-38(26-73)86-54(49(50)82)72-27-67-35-13-9-30(74)21-37(35)72;/h9,13,21,23,27,31-34,38,49-50,53-54,73,82H,10-12,14-20,22,24-26H2,1-8H3,(H16,60,61,62,63,64,65,66,68,69,70,71,74,75,76,77,78,79,80,81,83,84);/q;+4/p-1/t31-,32-,33-,34+,38-,49-,50-,53-,54+,56-,57+,58+,59+;/m1./s1
InChIKeyAAUZIRDSHVCNMM-FZHFKLCOSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=C2C(C(C3(N2[Co]45[N+]6=C(C(=C7[N+]4=C(C=C8[N+]5=C1C(C8CCC(=O)N)(C)CC(=O)N)C(C7CCC(=O)N)(C)C)C)C(C(C36)CC(=O)N)(C)CCC(=O)NCCOP(=O)(O)OC9C(OC(C9O)n1cnc2c1cc(cc2)O)CO)C)(C)CC(=O)N)CCC(=O)N
CC1=C2[C@H]([C@]([C@]3(N2[Co]45[N+]6=C(C(=C7[N+]4=C(C=C8[N+]5=C1[C@@]([C@@H]8CCC(=O)N)(C)CC(=O)N)C([C@@H]7CCC(=O)N)(C)C)C)[C@]([C@H]([C@H]36)CC(=O)N)(C)CCC(=O)NCCOP(=O)(O)O[C@@H]9[C@H](O[C@@H]([C@@H]9O)n1cnc2c1cc(cc2)O)CO)C)(C)CC(=O)N)CCC(=O)N
CC1=C2[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@]3(C)[C@H]4[C@H](CC(N)=O)[C@@](C)(CCC(=O)NCCO[P](O)(=O)O[C@H]5[C@@H](O)[C@H](O[C@@H]5CO)n6cnc7ccc(O)cc67)C8=[N@@+]4[Co]9([N@]23)[N@+]%10=C1[C@@](C)(CC(N)=O)[C@H](CCC(N)=O)C%10=CC%11=[N@@+]9C(=C8C)[C@@H](CCC(N)=O)C%11(C)C
CC1=C2[CH](CCC(N)=O)[C](C)(CC(N)=O)[C]3(C)[CH]4[CH](CC(N)=O)[C](C)(CCC(=O)NCCO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO)n6cnc7ccc(O)cc67)C8=[N+]4[Co]9([N]23)[N+]%10=C1[C](C)(CC(N)=O)[CH](CCC(N)=O)C%10=CC%11=[N+]9C(=C8C)[CH](CCC(N)=O)C%11(C)C
FormulaC59 H83 Co N13 O15 P
Name 6-hydroxybenzimidazolyl-norcobamide
ChEMBL
DrugBank
ZINC
PDB chain5obp Chain B Residue 503 [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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PDB5obp Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans.
Resolution1.593 Å
Binding residue
(original residue number in PDB)		Y31 T36 A37 F38 Y170 Y246 M249 N272 Q276 S277 V278 A289 M292 G293 A294 C295 V304 R305 L306 H357 N358 Q359 K362 Q364 Y369 C372 W376 Y382 C386
Binding residue
(residue number reindexed from 1)		Y24 T29 A30 F31 Y163 Y239 M242 N265 Q269 S270 V271 A282 M285 G286 A287 C288 V297 R298 L299 H350 N351 Q352 K355 Q357 Y362 C365 W369 Y375 C379
Annotation score1
Enzymatic activity
Enzyme Commision number 1.21.99.5: tetrachloroethene reductive dehalogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5obp, PDBe:5obp, PDBj:5obp
PDBsum5obp
PubMed29378885
UniProtO68252|PCEA_SULMU Tetrachloroethene reductive dehalogenase (Gene Name=pceA)

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