Structure of PDB 6q2e Chain A Binding Site BS02

Receptor Information

>6q2e Chain A (length=330) Species: 2173 (Methanobrevibacter smithii)

HMSMYNMDLDKVIRKINKKGARTVGLQFPEGLKMQAVKIAKAIESQTPAT
VIISGDPCFGACDVSDYKMKGSVDLIVHYGHTPLPLKYEVPTLFIEAFSN
IDVKKDLEKCLEKLEDYSKIALVTTTQHLHLLNEIKDYLEDNGKEVVLGS
SKNTKKGQVLGCNFSSIKNLDAEVYLFIGSGNFHPLGIYLFTKSPVLALD
PYNSEIRDISAFADRILRIRFARITKAREAEKWGIIVSSKEGQYRMKLAK
EIKKILEDNKMEAYIIMADNINPDILLPYMELDAFVVSACPRIAIDDSQM
YKKPLLTPQELEIVLNKRQWENYQLDEILF

Ligand information

• Ligand ID: SF4
• InChI: InChI=1S/4Fe.4S
• InChIKey: LJBDFODJNLIPKO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
  CACTVS 3.385: S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
• Formula: Fe4 S4
• Name: IRON/SULFUR CLUSTER
• PDB chain: 6q2e Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q2e The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
• Resolution: 1.768 Å
• Binding residue (original residue number in PDB): F58 C61 G160 C161 Q242 C289 R291
• Binding residue (residue number reindexed from 1): F59 C62 G161 C162 Q243 C290 R292
• Annotation score: 1

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

External links

• PDB: RCSB:6q2e, PDBe:6q2e, PDBj:6q2e
• PDBsum: 6q2e
• PubMed: 31566354
• UniProt: A5UMY5