Structure of PDB 6m2f Chain A Binding Site BS01

Receptor Information
>6m2f Chain A (length=121) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEALVLVGHGSRLPYSKELLVKLAEKVKERNLFPIVEIGLMEFSEPTIPQ
AVKKAIEQGAKRIIVVPVFLAHGIHTTRDIPRLLGLIEDLEIPEDVEIIY
REPIGADDRIVDIIIDRAFGR
Ligand information
Ligand IDF0L
InChIInChI=1S/C42H46N4O16.Ni/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29;/h13-16,23-24H,3-12,17-18H2,1-2H3,(H10,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62);/q;+4/p-2/t23-,24-,41+,42+;/m1./s1
InChIKeyMENOACMQLVBAQR-QIISWYHFSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@@]1([C@@H](C2=[N]3C1=Cc4c(c(c5n4[Ni+2]36[N]7=C(C=C8N6C(=C2)[C@@]([C@@H]8CCC(=O)O)(C)CC(=O)O)C(=C(C7=C5)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
CACTVS 3.385C[C]1(CC(O)=O)[CH](CCC(O)=O)C2=NC1=Cc3n4[Ni++][N]5C(=CC6=NC(=Cc4c(CCC(O)=O)c3CC(O)=O)C(=C6CC(O)=O)CCC(O)=O)[CH](CCC(O)=O)[C](C)(CC(O)=O)C5=C2
OpenEye OEToolkits 2.0.7CC1(C(C2=[N]3C1=Cc4c(c(c5n4[Ni+2]36[N]7=C(C=C8N6C(=C2)C(C8CCC(=O)O)(C)CC(=O)O)C(=C(C7=C5)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
CACTVS 3.385C[C@]1(CC(O)=O)[C@H](CCC(O)=O)C2=NC1=Cc3n4[Ni++][N@]5C(=CC6=NC(=Cc4c(CCC(O)=O)c3CC(O)=O)C(=C6CC(O)=O)CCC(O)=O)[C@@H](CCC(O)=O)[C@](C)(CC(O)=O)C5=C2
FormulaC42 H44 N4 Ni O16
Namenickel-sirohydrochlorin
ChEMBL
DrugBank
ZINC
PDB chain6m2f Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6m2f The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H9 S11 R12 F69 L70 G73 I74 H75
Binding residue
(residue number reindexed from 1)		H9 S11 R12 F69 L70 G73 I74 H75
Annotation score3
Enzymatic activity
Enzyme Commision number 4.99.1.11: sirohydrochlorin nickelchelatase.
4.99.1.3: sirohydrochlorin cobaltochelatase.
Gene Ontology
Molecular Function
GO:0016151 nickel cation binding
GO:0016829 lyase activity
GO:0016852 sirohydrochlorin cobaltochelatase activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
Biological Process
GO:0009236 cobalamin biosynthetic process
GO:0015948 methanogenesis
GO:0019251 anaerobic cobalamin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6m2f, PDBe:6m2f, PDBj:6m2f
PDBsum6m2f
PubMed34163982
UniProtQ58380|CFBA_METJA Sirohydrochlorin cobaltochelatase (Gene Name=cbiX)

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