Structure of PDB 5ma2 Chain A Binding Site BS03

Receptor Information

>5ma2 Chain A (length=445) Species: 66821 (Sulfurospirillum multivorans)

AEKEKNAAEIRQQFAMTAGSPIIVNDKLERYAEVRTAFTHPTSFFKPNYK
GEVKPWFLSAYDEKVRQIENGENGPKMKAKNVGEARAGRALEAAGWTLDI
NYGNIYPNRFFMLWSGETMTNTQLWAPVGLDRRPPDTTDPVELTNYVKFA
ARMAGADLVGVARLNRNWVYSEAVTIPADVPYEQSLHKEIEKPIVFKDVP
LPIETDDELIIPNTCENVIVAGIAMNREMMQTAPNSMACATTAFCYSRMC
MFDMWLCQFIRYMGYYAIPSCNGVGQSVAFAVEAGLGQASRMGACITPEF
GPNVRLTKVFTNMPLVPDKPIDFGVTEFCETCKKCARECPSKAITEGPRT
FEGRSIHNQSGKLQWQNDYNKCLGYWPESGGYCGVCVAVCPFTKGNIWIH
DGVEWLIDNTRFLNITEVWDGKINTYGLDADHFRDTVSFRKDRVK

Ligand information

• Ligand ID: BVQ
• InChI: InChI=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
• InChIKey: XZMFKDUDYMLUGK-GVNDBXLGSA-M
• SMILES:
  OpenEye OEToolkits 1.7.6: CC1=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
• Formula: C57 H82 Co N16 O14 P
• Name: NORPSEUDO-B12
• PDB chain: 5ma2 Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ma2 Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer.
• Resolution: 1.879 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
• Binding residue (residue number reindexed from 1): 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
• Annotation score: 1

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

External links

• PDB: RCSB:5ma2, PDBe:5ma2, PDBj:5ma2
• PDBsum: 5ma2
• PubMed: 28671181
• UniProt: O68252|PCEA_SULMU Tetrachloroethene reductive dehalogenase (Gene Name=pceA)