Structure of PDB 6q2e Chain B Binding Site BS01

Receptor Information
>6q2e Chain B (length=329) Species: 2173 (Methanobrevibacter smithii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMYNMDLDKVIRKINKKGARTVGLQFPEGLKMQAVKIAKAIESQTPATVI
ISGDPCFGACDVSDYKMKGSVDLIVHYGHTPLPLKYEVPTLFIEAFSNID
VKKDLEKCLEKLEDYSKIALVTTTQHLHLLNEIKDYLEDNGKEVVLGSSK
NTKKGQVLGCNFSSIKNLDAEVYLFIGSGNFHPLGIYLFTKSPVLALDPY
NSEIRDISAFADRILRIRFARITKAREAEKWGIIVSSKEGQYRMKLAKEI
KKILEDNKMEAYIIMADNINPDILLPYMELDAFVVSACPRIAIDDSQMYK
KPLLTPQELEIVLNKRQWENYQLDEILFH
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 chain6q2e Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6q2e The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
Resolution1.768 Å
Binding residue
(original residue number in PDB)		F58 K239 Q242 N269 I270 C289 R291 I292 D295 D296
Binding residue
(residue number reindexed from 1)		F57 K238 Q241 N268 I269 C288 R290 I291 D294 D295
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:6q2e, PDBe:6q2e, PDBj:6q2e
PDBsum6q2e
PubMed31566354
UniProtA5UMY5

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