Structure of PDB 4ffp Chain A Binding Site BS03

Receptor Information

>4ffp Chain A (length=353) Species: 269797 (Methanosarcina barkeri str. Fusaro)

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPD
TLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPL
FRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSS
GINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSD
YGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFG
AVL

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 4ffp Chain A Residue 903

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ffp Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): S136 S137 E227 E239 D241 R243
• Binding residue (residue number reindexed from 1): S136 S137 E221 E233 D235 R237
• 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:4ffp, PDBe:4ffp, PDBj:4ffp
• PDBsum: 4ffp
• PubMed: 22985965
• UniProt: Q46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)