Structure of PDB 6npd Chain A Binding Site BS01

Receptor Information

>6npd Chain A (length=378) Species: 506591 (Leisingera caerulea)

HHMPRSVTADASGSFLTLTFEDGSESRFHAIWLRDNALDPETRSPGNGQR
LITIGDIPADTRISTALVDDGALTVTFAPEGKTVTFPGKWLKSNAYDTDQ
SSEVGRTSPDVETWDSSQPAPAFDWNEVQSDPKAKRDWLDAIARLGFAKL
VNGPVREGALIECASMFGFVRETNYGKYFEVRTEVNPTNLAYTGLGLQAH
TDNPYRDPVPSLQILYCLENSAEGGDSIVVDGFRAAERLRDEDPEGFALL
AGNPARFEYKGSDGVHLRARRPMIELSPDGEMIAIRFNNRSSAPFVDIPF
EKMEAYYAAYRRLGEFIDDPEMGVSFKLEPGESFIVDNTRVLHARLGYSG
SGSRWLQGCYADKDGLFSTLNVLNAQLG

Ligand information

• Ligand ID: FE2
• InChI: InChI=1S/Fe/q+2
• InChIKey: CWYNVVGOOAEACU-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Fe+2]
  CACTVS 3.341: [Fe++]
• Formula: Fe
• Name: FE (II) ION
• DrugBank: DB14510
• PDB chain: 6npd Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6npd A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): H198 D200 H341
• Binding residue (residue number reindexed from 1): H200 D202 H343
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.11.72: [2-(trimethylamino)ethyl]phosphonate dioxygenase.

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0008336 gamma-butyrobetaine dioxygenase activity
• GO:0016491 oxidoreductase activity
• GO:0016706 2-oxoglutarate-dependent dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0045329 carnitine biosynthetic process

External links

• PDB: RCSB:6npd, PDBe:6npd, PDBj:6npd
• PDBsum: 6npd
• PubMed: 30789718
• UniProt: A0A4V8H042|TMPA_LEICA [2-(trimethylamino)ethyl]phosphonate dioxygenase (Gene Name=tmpA)