Structure of PDB 6bxk Chain A Binding Site BS01

Receptor Information
>6bxk Chain A (length=340) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LHEIPKSEILKELKRIGAKRVLIQSPEGLRREAEELAGFLEENNIEVFLH
GEINYGACDPADREAKLVGCDALIHLGHSYMKLPLEVPTIFVPAFARVSV
VEALKENIGEIKKLGRKIIVTTTAQHIHQLKEAKEFLESEGFEVSIGRGD
SRISWPGQVLGCNYSVAKVRGEGILFIGSGIFHPLGLAVATRKKVLAIDP
YTKAFSWIDPERFIRKRWAQIAKAMDAKKFGVIVSIKKGQLRLAEAKRIV
KLLKKHGREARLIVMNDVNYHKLEGFPFEAYVVVACPRVPLDDYGAWRKP
VLTPKEVEILLGLREEYEFDEILGGPRESDEPFGISIHST
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 chain6bxk Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6bxk Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Resolution2.347 Å
Binding residue
(original residue number in PDB)		Y56 S236 K238 Q241 V269 C287 R289
Binding residue
(residue number reindexed from 1)		Y55 S235 K237 Q240 V268 C286 R288
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:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
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
GO:0050843 S-adenosylmethionine catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6bxk, PDBe:6bxk, PDBj:6bxk
PDBsum6bxk
PubMed29590073
UniProtO58832|DPH2_PYRHO 2-(3-amino-3-carboxypropyl)histidine synthase (Gene Name=dph2)

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