Structure of PDB 8gf5 Chain A Binding Site BS02

Receptor Information
>8gf5 Chain A (length=560) Species: 188937 (Methanosarcina acetivorans C2A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AADIFAKFKKSMEVKFTQEYGSNKQAGGDITGKTEKFLRLGPEQDARKQE
MIKAGKEIAEKRGIAFYNPMMHMGAPLGQRAITPYTISGTDIVAEPDDLH
YVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLETLN
HAMPGAETHPALVDDCYVKIFTGDDELADEIDKQYVINVNKMFSEEQAAQ
IKASIGKTTWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGE
AAVADLSFAAKHAALVSMGEMLPARRARGPNEPGGLSFGHLSDIVQTSRV
SKDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTDDILDNN
TYYDVDYINDKYNGAANLGTDNKVKATLDVVKDIATESTLYGIETYEKFP
TALEDHFGGSQRATVLAAASGVACALATGNANAGLSGWYLSMYVHKEAWG
RLGFFGFDLQDQCGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQGGYA
GIAQAAHSGRGDAFTVNPLLKVCFADELMPFNFAEPRREFGRGAIREFMP
AGERSLVIPA
Ligand information
Ligand IDF43
InChIInChI=1S/C42H52N6O13.Ni/c1-40(16-30(43)50)22(5-9-33(54)55)27-15-42-41(2,17-31(51)48-42)23(6-10-34(56)57)26(47-42)13-24-20(11-35(58)59)19(4-8-32(52)53)39(45-24)37-28(49)7-3-18-21(12-36(60)61)25(46-38(18)37)14-29(40)44-27;/h13,18-23,25,27H,3-12,14-17H2,1-2H3,(H9,43,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61);/q;+2/p-1/t18-,19-,20-,21-,22+,23+,25+,27-,40-,41-,42-;/m0./s1
InChIKeyXLFIRMYGVLUNOY-SXMZNAGASA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@@]12CC(=O)N[C@@]13C[C@H]4[C@H]([C@](C5=[N]4[Ni+]67[N]3=C([C@H]2CCC(=O)O)C=C8N6C(=C9C(=O)CC[C@@H]1C9=[N]7[C@H](C5)[C@H]1CC(=O)O)[C@H]([C@@H]8CC(=O)O)CCC(=O)O)(C)CC(=O)N)CCC(=O)O
OpenEye OEToolkits 1.7.6CC12CC(=O)NC13CC4C(C(C5=[N]4[Ni+]67[N]3=C(C2CCC(=O)O)C=C8N6C(=C9C(=O)CCC1C9=[N]7C(C5)C1CC(=O)O)C(C8CC(=O)O)CCC(=O)O)(C)CC(=O)N)CCC(=O)O
CACTVS 3.385C[C@]1(CC(N)=O)[C@H](CCC(O)=O)[C@@H]2C[C@]34NC(=O)C[C@@]3(C)[C@H](CCC(O)=O)C5=N4|[Ni+]|67|N2=C1C[C@H]8N|6=C9[C@@H](CCC(=O)C9=C%10[C@@H](CCC(O)=O)[C@H](CC(O)=O)C(=C5)[N@@]7%10)[C@@H]8CC(O)=O
CACTVS 3.385C[C]1(CC(N)=O)[CH](CCC(O)=O)[CH]2C[C]34NC(=O)C[C]3(C)[CH](CCC(O)=O)C5=N4|[Ni+]|67|N2=C1C[CH]8N|6=C9[CH](CCC(=O)C9=C%10[CH](CCC(O)=O)[CH](CC(O)=O)C(=C5)[N]7%10)[CH]8CC(O)=O
FormulaC42 H51 N6 Ni O13
NameFACTOR 430
ChEMBL
DrugBank
ZINC
PDB chain8gf5 Chain A Residue 602 [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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PDB8gf5 McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		G340 V341 G342 F343 T344 Q345 Y346 F416 F463
Binding residue
(residue number reindexed from 1)		G331 V332 G333 F334 T335 Q336 Y337 F407 F454
Annotation score1
Enzymatic activity
Enzyme Commision number 2.8.4.1: coenzyme-B sulfoethylthiotransferase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0050524 coenzyme-B sulfoethylthiotransferase activity
Biological Process
GO:0015948 methanogenesis
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8gf5, PDBe:8gf5, PDBj:8gf5
PDBsum8gf5
PubMed37307484
UniProtQ8THH1|MCRA_METAC Methyl-coenzyme M reductase subunit alpha (Gene Name=mcrA)

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