Structure of PDB 6bxm Chain B Binding Site BS03

Receptor Information
>6bxm Chain B (length=314) Species: 1392998 (Candidatus Methanoperedens nitroreducens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDLERILKTIKDKNCKKVGLQFPEGLKRQAINIAREIEEKTRANVIISGN
PCFGACDIDTILAGSVDILFHFGHAGMGEYENVVFIEARSNIDIIPAVKT
ALNLLKANRIGLITTVQHVHKLEEACKVIKEYGKECVIGKPRAIYPGQVL
GCNFTAARVDCEEFIYIGSGIFHPLGVAIATKKRVIAADPFLNQAVEVSP
ERFLRKRGGYIAKATGAKIFGIIVSTKSGQYRMKLAQKLKEIADKHGKIG
YIILMDLVTPEQLLAFKADAYVNTACPRITIDDAERFHAPVLTPQEFEIV
LGERRWENMEMDEM
Ligand information
Ligand IDMTA
InChIInChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyWUUGFSXJNOTRMR-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
FormulaC11 H15 N5 O3 S
Name5'-DEOXY-5'-METHYLTHIOADENOSINE
ChEMBLCHEMBL277041
DrugBankDB02282
ZINCZINC000004228245
PDB chain6bxm Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6bxm Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Resolution2.252 Å
Binding residue
(original residue number in PDB)		F58 K234 Q237 L264 V265 C283 I286 D290
Binding residue
(residue number reindexed from 1)		F53 K227 Q230 L257 V258 C276 I279 D283
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:6bxm, PDBe:6bxm, PDBj:6bxm
PDBsum6bxm
PubMed29590073
UniProtA0A062UZ78

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