Structure of PDB 5n28 Chain D Binding Site BS03

Receptor Information
>5n28 Chain D (length=547) Species: 647171 (Methanotorris formicicus Mc-S-70) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKLFLKALKEKFEEDPKEKYTKFYVFGGWRQSARKREFVEAAEKLAEKRG
GIPFYNPDIGVPLGQRKLMPYKLSGTDYIVEGDDLHFMNNAAMQQFWDDI
RRTVIVGMDTAHAVLEKRLGVEVTPETINEYMETINHALPGGAVVQEHMV
EVHPALAWDCYAKIFTGDDELADEIDKKFLIDINKLFPEEQAEQLKAAIG
KRTYQVSRVPTLVGRVCDGGTIARWSAMQIGMSFITAYKLCAGEAAIADF
SYAAKHADVIQMGTLLPARRARGPNEPGGIPFGILADVVQTTRVSDDPVE
QSLEVVASGAMLYDQIWLGSYMSGGVGFTQYATASYTDDILDDFSYYGYD
YVEKKYGICGAKPTMDVVEDIATEVTLYALECYDEFPALLEDHFGGSQRA
AVAAAASGISVCMATGNSNAGLNGWYLSQILHKEYHSRLGFYGYDLQDQC
GASNSLSIRNDESSPLELRGPNYPNYAMNVGHQGEYAGITQAAHSARKDA
FALNPLIKVAFADPSLVFDFSHPRKEFARGALREFEPAGERDPIIPA
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 chain5n28 Chain A Residue 604 [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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PDB5n28 Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		V330 G331 F332 T333 Q334 Y335 F398 G444 F445
Binding residue
(residue number reindexed from 1)		V326 G327 F328 T329 Q330 Y331 F394 G440 F441
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q150 Y335 G447 N483
Catalytic site (residue number reindexed from 1) Q146 Y331 G443 N479
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5n28, PDBe:5n28, PDBj:5n28
PDBsum5n28
PubMed28559298
UniProtH1KXL5

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