Structure of PDB 6bxn Chain B Binding Site BS02

Receptor Information
>6bxn Chain B (length=316) Species: 1392998 (Candidatus Methanoperedens nitroreducens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLERILKTIKDKNCKKVGLQFPEGLKRQAINIAREIEEKTRANVIISGNP
CFGACDIDTILAGSVDILFHFGHAGMGEYENVVFIEARSNIDIIPAVKTA
LNLLKANRIGLITTVQHVHKLEEACKVIKEYGKECVIGKGDPRAIYPGQV
LGCNFTAARVDCEEFIYIGSGIFHPLGVAIATKKRVIAADPFLNQAVEVS
PERFLRKRGGYIAKATGAKIFGIIVSTKSGQYRMKLAQKLKEIADKHGKI
GYIILMDLVTPEQLLAFKADAYVNTACPRITIDDAERFHAPVLTPQEFEI
VLGERRWENMEMDEMI
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain6bxn Chain B Residue 901 [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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PDB6bxn Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Resolution2.079 Å
Binding residue
(original residue number in PDB)		F58 H180 K234 Q237 L264 V265 C283 I286 D289 D290
Binding residue
(residue number reindexed from 1)		F52 H174 K228 Q231 L258 V259 C277 I280 D283 D284
Annotation score5
Enzymatic activity
Enzyme Commision number 2.5.1.108: 2-(3-amino-3-carboxypropyl)histidine synthase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0090560 2-(3-amino-3-carboxypropyl)histidine synthase activity
Biological Process
GO:0017183 protein histidyl modification to diphthamide

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6bxn, PDBe:6bxn, PDBj:6bxn
PDBsum6bxn
PubMed29590073
UniProtA0A062UZ78

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