Structure of PDB 4ffm Chain A Binding Site BS04

Receptor Information

>4ffm Chain A (length=344) Species: 269797 (Methanosarcina barkeri str. Fusaro)

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKARIIYGLEPDTLVEEYVEG
EVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPLFRQISHDLA
ANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSSGINLIELLF
RAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSDYGKFYEEPG
IEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFGAVL

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 4ffm Chain A Residue 904

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ffm Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Resolution: 1.91 Å
• Binding residue (original residue number in PDB): E239 D241
• Binding residue (residue number reindexed from 1): E224 D226
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 6.3.2.59: 3-methyl-D-ornithine--L-lysine ligase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008652 amino acid biosynthetic process
• GO:0071524 pyrrolysine biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:4ffm, PDBe:4ffm, PDBj:4ffm
• PDBsum: 4ffm
• PubMed: 22985965
• UniProt: Q46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)