Structure of PDB 1e6y Chain A Binding Site BS04

Receptor Information
>1e6y Chain A (length=568) Species: 2208 (Methanosarcina barkeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AADIFSKFKKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVE
MIKAGKEIAEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLH
YVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLN
HAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKE
FSEEQAAQIKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFIS
AYAMCAGEAAVADLSFAAKHAALVSMGEMLPARRARGPNEPGGLSFGHLS
DIVQTSRVSEDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAY
TDDILDNNTYYDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYG
IETYEKFPTALEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSM
YLHKEAWGRLGFFGFDLQDQCGATNVLSYQGDEGLPDELRGPNYPNYAMN
VGHQGGYAGIAQAAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGR
GAIREFVPAGERSLVIPA
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 chain1e6y Chain D Residue 5570 [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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PDB1e6y Comparison of Three Methyl-Coenzyme M Reductases from Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation
Resolution1.6 Å
Binding residue
(original residue number in PDB)		V1341 G1342 F1343 T1344 Q1345 Y1346 F1463
Binding residue
(residue number reindexed from 1)		V340 G341 F342 T343 Q344 Y345 F462
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y1346 G1465 N1501
Catalytic site (residue number reindexed from 1) Y345 G464 N500
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:1e6y, PDBe:1e6y, PDBj:1e6y
PDBsum1e6y
PubMed11023796
UniProtP07962|MCRA_METBF Methyl-coenzyme M reductase subunit alpha (Gene Name=mcrA)

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