Structure of PDB 6q2d Chain B Binding Site BS01

Receptor Information
>6q2d Chain B (length=325) Species: 2173 (Methanobrevibacter smithii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NMDLDKVIRKINKKGARTVGLQFPEGLKMQAVKIAKAIESQTPATVIISG
DPCFGACDVSDYKMKGSVDLIVHYGHTPLPLKYEVPTLFIEAFSNIDVKK
DLEKCLEKLEDYSKIALVTTTQHLHLLNEIKDYLEDNGKEVVLGSSKNTK
KGQVLGCNFSSIKNLDAEVYLFIGSGNFHPLGIYLFTKSPVLALDPYNSE
IRDISAFADRILRIRFARITKAREAEKWGIIVSSKEGQYRMKLAKEIKKI
LEDNKMEAYIIMADNINPDILLPYMELDAFVVSACPRIAIDDSQMYKKPL
LTPQELEIVLNKRQWENYQLDEILF
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain6q2d 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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PDB6q2d The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		C61 G160 C161 C289 R291
Binding residue
(residue number reindexed from 1)		C57 G156 C157 C285 R287
Annotation score1
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:6q2d, PDBe:6q2d, PDBj:6q2d
PDBsum6q2d
PubMed31566354
UniProtA5UMY5

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