Structure of PDB 5m8w Chain B Binding Site BS03

Receptor Information
>5m8w Chain B (length=419) Species: 66821 (Sulfurospirillum multivorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYKGEVKPW
FLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDINYGNIY
PNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFAARMAGA
DLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVPLPIETD
DELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMCMFDMWL
CQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEFGPNVRL
TKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRTFEGRSI
HNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKNITEVWDGKINT
YGLDADHFRDTVSFRKDRV
Ligand information
Ligand IDBVQ
InChIInChI=1S/C57H83N16O14P.Co/c1-26-42-29(10-13-36(59)76)53(3,4)34(70-42)20-32-28(9-12-35(58)75)55(6,21-39(62)79)48(69-32)27(2)43-30(11-14-37(60)77)56(7,22-40(63)80)57(8,72-43)49-31(19-38(61)78)54(5,47(26)71-49)16-15-41(81)65-17-18-85-88(83,84)87-46-33(23-74)86-52(45(46)82)73-25-68-51-44(73)50(64)66-24-67-51;/h20,24-25,28-31,33,45-46,49,52,74,82H,9-19,21-23H2,1-8H3,(H17,58,59,60,61,62,63,64,65,66,67,69,70,71,72,75,76,77,78,79,80,81,83,84);/q;+6/p-1/t28-,29-,30-,31+,33-,45-,46-,49-,52+,54-,55+,56+,57+;/m1./s1
InChIKeyXZMFKDUDYMLUGK-GVNDBXLGSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=C2C(C(C3=CC4=[N+]5C(=C(C6=[N+]7[Co+2]5(N32)[N+]8=C1C(C(C8C7(C(C6CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)(C)CCC(=O)NCCOP(=O)(O)OC9C(OC(C9O)n1cnc2c1c(ncn2)N)CO)C)C(C4CCC(=O)N)(C)CC(=O)N)(C)C)CCC(=O)N
CC1=C2[C@@H](CCC(N)=O)C(C)(C)C3=CC4=[N@+]5C(=C(C)C6=[N@+]7[C@@](C)([C@H]8[C@H](CC(N)=O)[C@@](C)(CCC(=O)NCCO[P](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11ncnc(N)c%10%11)C1=[N@+]8[Co@++]57[N@]23)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O
CC1=C2[C@@]([C@@H](C3=[N+]2[Co@@+2]45N6C(=C3)C([C@@H](C6=C(C7=[N+]4[C@H]([C@@H]([C@@]7(C)CCC(=O)NCCOP(=O)(O)O[C@@H]8[C@H](O[C@@H]([C@@H]8O)n9cnc2c9c(ncn2)N)CO)CC(=O)N)[C@@]2([N+]5=C1[C@H]([C@]2(C)CC(=O)N)CCC(=O)N)C)C)CCC(=O)N)(C)C)CCC(=O)N)(C)CC(=O)N
CC1=C2[CH](CCC(N)=O)C(C)(C)C3=CC4=[N+]5C(=C(C)C6=[N+]7[C](C)([CH]8[CH](CC(N)=O)[C](C)(CCC(=O)NCCO[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11ncnc(N)c%10%11)C1=[N+]8[Co++]57[N]23)[C](C)(CC(N)=O)[CH]6CCC(N)=O)[C](C)(CC(N)=O)[CH]4CCC(N)=O
FormulaC57 H82 Co N16 O14 P
NameNORPSEUDO-B12
ChEMBL
DrugBank
ZINC
PDB chain5m8w 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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PDB5m8w Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer.
Resolution2.279 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)		Y25 T30 A31 F32 Y164 Y240 M243 N266 Q270 S271 V272 A283 M286 G287 A288 C289 V298 R299 L300 H351 N352 Q353 K356 Q358 Y363 C366 W370 Y376 C380
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:5m8w, PDBe:5m8w, PDBj:5m8w
PDBsum5m8w
PubMed28671181
UniProtO68252|PCEA_SULMU Tetrachloroethene reductive dehalogenase (Gene Name=pceA)

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